Contacts of the helix formed by residues 5 - 28 (chain K) in PDB entry 6AHR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 5 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K PRO* 1.3 88.7 - - + +
6K LYS* 1.3 59.1 + - - +
8K ARG* 3.1 13.6 + - + +
9K GLU* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LYS* 4.7 27.8 - - + +
4K PRO 4.5 1.9 - - - -
5K VAL* 1.3 80.1 - - - +
7K ASP* 1.3 61.4 + - - +
9K GLU* 3.4 11.3 + - + +
10K ALA* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 7 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 3.8 13.9 + - - +
4K PRO* 4.0 14.1 + - + +
5K VAL 3.3 0.2 - - - -
6K LYS* 1.3 77.9 - - - +
8K ARG* 1.3 60.0 + - - +
10K ALA* 3.2 6.6 + - - +
11K PHE* 3.0 56.1 + - + -
51K LEU* 3.3 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C LEU* 4.3 24.5 - - - +
221C THR* 4.5 23.1 + - + +
4K PRO 3.3 17.9 + - - +
5K VAL* 3.1 13.2 + - - +
7K ASP* 1.3 75.1 - - - +
9K GLU* 1.3 62.7 + - - +
11K PHE* 3.5 17.4 - - + +
12K GLN* 2.6 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 5.1 5.5 - - - +
129D LYS* 2.7 34.4 + - - +
132D LYS* 4.6 15.0 - - + +
5K VAL* 2.9 30.9 + - + +
6K LYS* 3.4 14.8 - - + +
7K ASP 3.2 0.2 - - - -
8K ARG* 1.3 84.8 + - - +
10K ALA* 1.3 62.1 + - - +
12K GLN* 3.1 26.6 + - - +
13K ARG* 3.2 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D SER* 4.9 10.5 - - - +
6K LYS 3.3 9.0 + - - +
7K ASP* 3.2 14.2 + - - +
9K GLU* 1.3 74.9 - - - +
11K PHE* 1.3 62.4 + - + +
12K GLN 3.2 0.2 - - - -
13K ARG* 3.2 18.5 + - + +
14K LEU* 2.9 29.9 + - - +
45K ILE* 5.8 7.9 - - + +
49K LEU* 5.6 8.5 - - + -
51K LEU* 5.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 4.0 26.0 - - - -
25C LEU* 3.6 57.1 - - + +
221C THR* 3.6 30.1 - - + -
4K PRO 6.0 0.2 - - - -
7K ASP* 3.0 49.7 + - - -
8K ARG* 3.5 16.8 - - + +
9K GLU 3.2 0.6 - - - -
10K ALA* 1.3 77.9 - - - +
12K GLN* 1.3 60.5 - - - +
14K LEU* 3.4 1.3 + - + -
15K ASN* 3.0 35.5 + - - +
51K LEU* 3.6 23.3 - - + -
52K ARG 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU* 6.5 0.4 - - + -
219C LEU* 3.3 43.5 - - + +
221C THR* 5.5 1.6 - - - +
109D TYR* 3.2 22.9 + - + +
112D ASP 6.0 0.7 - - - +
113D LEU* 5.0 10.9 - - + +
8K ARG* 2.6 42.7 + - - +
9K GLU* 3.1 27.4 + - - +
11K PHE* 1.3 81.8 - - - +
13K ARG* 1.3 58.8 + - - +
15K ASN* 2.8 19.8 - - - +
16K PHE* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D TYR* 3.2 19.5 + - + +
113D LEU* 4.0 9.0 - - - +
128D ALA 4.4 0.2 + - - -
129D LYS* 3.7 24.5 + - - +
132D LYS* 2.9 46.2 + - - +
133D ALA* 3.3 42.1 - - + +
134D ASP* 4.0 18.8 - - + +
208D SER* 4.6 4.1 + - - +
9K GLU* 3.2 37.3 + - - +
10K ALA* 3.2 15.7 + - + +
12K GLN* 1.3 76.9 - - - +
14K LEU* 1.3 59.6 + - - +
16K PHE* 3.5 5.8 - - + +
17K LEU* 3.0 35.3 + - - +
45K ILE* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.7 24.0 - - + -
27C ASN* 5.4 2.2 - - - +
10K ALA 2.9 16.6 + - - +
11K PHE* 3.8 4.0 - - + +
13K ARG* 1.3 77.0 - - - +
15K ASN* 1.3 58.7 + - + +
17K LEU* 3.3 11.7 + - - +
18K TYR* 3.0 25.0 + - + +
42K GLU* 3.3 45.4 - - + +
45K ILE* 4.5 24.2 - - + +
46K ALA* 4.8 11.0 - - + -
51K LEU* 4.7 16.6 - - + -
53K ARG* 6.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 4.3 7.7 - - + +
27C ASN* 3.5 31.7 + - - +
29C TYR* 3.7 22.4 + - + +
217C GLU* 5.5 7.7 - - - +
218C ASN 3.9 8.5 + - - -
219C LEU* 3.9 15.1 - - - +
109D TYR* 5.3 0.7 - - - -
11K PHE 3.0 19.0 + - - +
12K GLN* 2.8 30.0 - - - +
14K LEU* 1.3 75.6 - - - +
16K PHE* 1.3 60.7 + - - +
17K LEU 3.4 0.2 - - - -
18K TYR* 3.6 12.9 - - + +
19K GLN* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU* 6.3 0.7 - - - -
102D LEU 5.9 0.2 - - - -
105D LEU* 3.8 35.2 - - + -
106D TRP* 4.1 26.5 - + + -
109D TYR* 3.5 52.7 - + + -
134D ASP* 4.8 10.8 - - + -
136D HIS 3.9 20.4 - - - -
137D GLY* 5.1 0.9 - - - -
12K GLN 2.9 21.7 + - - +
13K ARG* 3.5 7.6 - - + +
15K ASN* 1.3 76.0 + - - +
17K LEU* 1.3 71.7 + - + +
19K GLN* 3.3 7.6 + - - +
20K ALA* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ASP* 3.4 27.1 - - + +
136D HIS* 4.2 30.3 - - + -
13K ARG 3.0 18.4 + - - +
14K LEU* 3.3 7.4 + - - +
16K PHE* 1.3 87.1 - - + +
18K TYR* 1.3 57.8 + - - +
20K ALA* 3.3 5.3 + - + +
21K ALA* 3.0 28.8 + - - +
38K TYR* 4.1 30.4 - - + +
41K THR* 3.9 21.3 - - + -
42K GLU* 4.3 15.9 - - + +
45K ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 18 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN* 5.5 12.3 - - + +
29C TYR* 6.0 7.6 - + - -
207C TRP* 3.4 27.0 - + - -
14K LEU* 3.0 11.6 + - + +
15K ASN* 3.6 15.5 - - + +
17K LEU* 1.3 77.5 - - - +
19K GLN* 1.3 61.3 + - + +
21K ALA* 3.5 6.4 + - - +
22K HIS* 3.1 60.1 + + - -
42K GLU* 3.5 33.3 + - - +
57K VAL* 3.4 22.9 - - + +
60K THR* 4.9 4.0 + - - -
61K LEU* 3.6 23.3 - - + +
68K LEU* 3.8 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TYR* 5.6 6.0 - - + -
207C TRP 5.9 2.7 - - - +
208C LEU 5.4 3.0 - - - +
215C SER* 3.4 29.9 - - - +
216C GLY 3.7 20.3 + - - +
217C GLU* 3.3 30.2 + - - +
105D LEU* 3.9 17.0 - - + +
15K ASN 2.9 17.6 + - - +
16K PHE* 3.9 8.5 - - - +
17K LEU 3.3 0.2 - - - -
18K TYR* 1.3 76.9 - - + +
20K ALA* 1.3 60.1 + - - +
22K HIS* 3.3 11.7 + - + +
23K CYS* 2.9 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU* 6.0 3.5 - - + +
105D LEU* 3.9 21.0 - - + +
136D HIS 6.1 0.4 - - - +
16K PHE* 2.9 26.1 + - + +
17K LEU* 3.3 8.7 + - + +
19K GLN* 1.3 74.3 - - - +
21K ALA* 1.3 60.2 + - - +
23K CYS* 3.2 3.1 + - - +
24K VAL* 2.9 33.5 + - + +
38K TYR* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K LEU 3.0 17.3 + - - +
18K TYR 3.6 6.3 - - - +
19K GLN 3.3 0.2 - - - -
20K ALA* 1.3 77.0 - - - +
22K HIS* 1.3 56.4 + - - +
24K VAL 3.4 0.9 + - - -
25K LEU* 3.0 35.7 + - - +
35K ALA* 3.7 30.1 - - + +
38K TYR* 4.2 6.2 - - + -
39K CYS 5.1 0.7 - - - +
68K LEU* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C TRP* 3.2 45.0 + + - +
208C LEU* 4.2 8.6 - - - +
18K TYR* 3.1 61.4 + + - -
19K GLN* 3.3 11.5 + - + +
21K ALA* 1.3 74.3 - - - +
23K CYS* 1.3 59.7 + - - +
25K LEU 3.8 0.6 - - - +
26K ALA* 2.9 33.3 + - - +
68K LEU* 3.5 18.6 - - + +
69K LEU* 3.4 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU 4.5 2.9 + - - +
209C GLN* 3.7 26.5 - - - +
101D PRO* 4.7 14.6 - - - -
102D LEU* 4.1 27.8 - - + -
105D LEU* 4.3 13.9 - - + -
19K GLN* 2.9 14.5 + - + +
20K ALA* 3.5 12.6 - - - +
22K HIS* 1.3 77.4 - - - +
24K VAL* 1.3 56.6 + - + +
26K ALA* 3.8 0.9 - - - +
27K GLN* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PHE* 6.0 2.7 - - + -
102D LEU* 4.7 15.0 - - + -
20K ALA 2.9 20.5 + - - +
21K ALA 3.7 3.8 - - - +
23K CYS* 1.3 76.9 - - - +
25K LEU* 1.3 63.8 + - + +
27K GLN* 3.2 13.7 + - - +
28K ASP* 3.2 18.7 + - + +
31K ASN 4.6 14.6 - - - +
32K GLN* 5.3 0.4 - - - -
34K LEU* 3.7 44.9 - - + +
35K ALA* 3.8 16.2 - - + +
38K TYR* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 5.3 0.9 - - - +
21K ALA 3.0 22.6 + - - +
24K VAL* 1.3 76.6 - - + +
26K ALA* 1.3 59.4 + - - +
28K ASP 4.1 12.9 - - - +
29K PRO* 5.3 2.1 - - + +
31K ASN 5.6 0.2 - - - +
32K GLN* 3.8 33.7 - - + +
35K ALA* 3.7 20.6 - - + -
68K LEU* 4.7 6.1 - - + +
69K LEU* 3.7 45.1 - - + +
70K VAL* 3.7 24.5 - - + +
73K LEU* 5.4 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 3.9 32.1 - - + -
209C GLN* 4.0 21.8 - - + +
22K HIS 2.9 17.8 + - - +
23K CYS 3.8 2.2 - - - +
25K LEU* 1.3 76.5 - - - +
27K GLN* 1.3 63.5 + - - +
28K ASP 5.3 0.2 - - - -
69K LEU* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLN* 4.9 9.0 - - - +
213C GLU* 5.8 0.6 + - - -
98D LEU* 3.1 67.0 + - + +
99D PHE* 5.1 9.2 - - + -
101D PRO* 4.1 18.8 - - - +
102D LEU* 5.3 4.5 - - + -
23K CYS* 2.9 24.6 + - - +
24K VAL* 3.2 6.5 + - - +
26K ALA* 1.3 81.9 - - - +
28K ASP* 1.3 63.6 + - + +
29K PRO* 4.3 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLN* 3.1 43.9 + - + +
98D LEU* 5.1 11.2 - - + +
99D PHE* 5.7 3.6 - - + -
24K VAL* 3.2 15.8 + - + +
25K LEU* 4.1 12.5 - - - +
27K GLN* 1.3 84.8 - - + +
29K PRO* 1.3 88.2 - - - +
30K GLU 4.1 0.3 + - - -
31K ASN* 3.5 19.5 + - - +
32K GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il