Contacts of the helix formed by residues 32 - 49 (chain K) in PDB entry 6AHU
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 GLN 32 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU* 3.8 25.4 - - + +
29K PRO* 6.2 0.2 - - - +
30K GLU* 4.0 12.7 - - - +
31K ASN* 1.3 80.0 - - - +
33K ALA* 1.3 61.3 + - - +
34K LEU 3.3 3.1 - - - +
35K ALA* 3.4 5.3 + - + +
36K ARG* 3.3 45.8 + - + +
70K VAL* 3.3 46.8 - - + +
73K LEU* 5.5 3.4 - - - +
74K THR* 4.0 18.2 + - - +
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Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 3.6 23.6 - - - +
86D LEU 3.9 9.4 - - - +
87D PHE* 3.6 27.6 - - + -
91D PRO* 6.2 2.0 - - + -
159D GLN* 4.1 3.1 - - - +
31K ASN 3.5 3.0 - - - -
32K GLN* 1.3 79.0 - - - +
34K LEU* 1.3 62.0 + - - +
36K ARG* 3.6 8.6 + - - +
37K PHE* 3.4 22.9 + - - +
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.7 30.1 - - + -
94D GLN* 5.4 2.0 - - - +
99D PHE* 4.8 12.3 - - + -
102D LEU* 4.9 2.0 - - + -
158D LEU* 3.7 43.3 - - + +
159D GLN* 3.7 11.9 - - - +
24K VAL* 3.8 42.8 - - + -
31K ASN 4.8 1.0 + - - +
32K GLN* 3.3 0.6 - - - +
33K ALA* 1.3 77.2 - - - +
35K ALA* 1.3 62.6 + - - +
36K ARG 3.3 0.2 - - - -
37K PHE* 4.3 0.2 - - - -
38K TYR* 3.2 41.3 + - + +
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Residues in contact with ALA 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA* 3.8 24.3 - - + +
24K VAL* 5.1 2.7 - - + +
25K LEU* 3.9 32.5 - - + -
32K GLN* 3.4 15.4 + - + +
33K ALA 3.4 0.2 - - - -
34K LEU* 1.3 76.6 - - - +
36K ARG* 1.3 62.7 + - + +
39K CYS* 3.5 22.2 + - - +
67K SER* 5.2 1.5 - - - -
68K LEU* 4.4 10.7 + - + +
69K LEU 6.0 0.4 - - - +
70K VAL* 5.1 6.5 - - + -
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Residues in contact with ARG 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU 6.0 0.7 - - - -
85D ARG* 5.2 17.3 - - + +
32K GLN* 3.3 40.6 + - + +
33K ALA* 4.1 8.1 - - - +
34K LEU 3.3 0.4 - - - -
35K ALA* 1.3 78.1 - - + +
37K PHE* 1.3 59.6 + - - +
39K CYS 3.4 0.2 + - - -
40K TYR* 2.9 22.2 + - - +
65K CYS* 3.5 12.4 - - - -
66K SER* 2.8 51.6 + - - +
67K SER* 4.8 8.9 - - - -
70K VAL* 5.3 4.9 - - + +
94K THR* 2.5 47.9 + - - +
201K ZN 4.5 1.8 - - - -
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Residues in contact with PHE 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 4.8 25.5 - - + +
136D HIS* 3.8 17.0 - + - -
159D GLN* 3.2 40.6 - - - +
160D GLU 3.2 44.2 - - - -
161D THR* 5.7 2.0 - - - -
204D SER* 5.6 1.1 - - - -
33K ALA 3.4 9.4 + - - +
34K LEU 4.4 1.6 - - - +
36K ARG* 1.3 76.6 - - - +
38K TYR* 1.3 74.5 + + - +
40K TYR* 4.2 19.5 - + - -
41K THR* 2.9 52.4 + - - -
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Residues in contact with TYR 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.3 13.9 - - + +
136D HIS* 4.0 28.6 - + + +
137D GLY 4.7 2.3 + - - -
157D LEU 4.5 2.4 + - - -
158D LEU* 3.4 34.4 + - - +
17K LEU* 3.4 39.0 - - + +
20K ALA* 3.8 40.6 - - + -
21K ALA* 3.8 9.2 - - + -
24K VAL* 4.4 11.2 - - + -
34K LEU* 3.2 30.1 + - + +
36K ARG 3.4 0.2 - - - -
37K PHE* 1.3 87.4 - + - +
39K CYS* 1.3 58.3 + - - +
41K THR* 4.1 2.8 - - - -
42K GLU* 3.3 23.6 + - - +
68K LEU* 5.0 0.4 - - - -
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Residues in contact with CYS 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ALA 3.5 17.0 + - - +
36K ARG 3.4 1.4 + - - -
37K PHE 3.2 0.4 - - - -
38K TYR* 1.3 78.8 - - - +
40K TYR* 1.3 58.5 + - - +
41K THR 3.3 0.4 - - - -
42K GLU* 3.3 8.7 + - - +
43K ARG* 2.9 29.4 + - - +
61K LEU* 3.8 44.1 - - - +
65K CYS 5.5 0.4 - - - -
66K SER* 3.7 21.8 - - - -
67K SER 4.3 2.9 - - - +
68K LEU* 3.7 19.0 - - + +
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Residues in contact with TYR 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A U 3.9 26.9 + - - -
122A G 5.1 8.3 + - - -
80D GLN* 3.9 17.9 + - - -
81D ARG* 5.8 1.0 + - - -
85D ARG* 6.2 5.6 - - - -
36K ARG 2.9 18.6 + - - +
37K PHE* 3.4 24.9 + + - +
39K CYS* 1.3 77.0 - - - +
41K THR* 1.3 56.8 + - - +
43K ARG* 3.4 35.5 + - - +
44K THR* 2.7 44.1 + - + -
65K CYS* 4.9 7.2 - - + -
66K SER* 4.0 8.4 - - - +
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ASP* 5.1 1.6 - - - +
136D HIS* 4.3 11.9 - - - +
204D SER* 5.3 1.1 - - - +
205D SER* 3.8 25.4 - - - +
17K LEU* 3.7 25.6 - - + -
37K PHE* 2.9 42.2 + - + -
38K TYR* 4.3 2.7 - - - -
40K TYR* 1.3 76.7 - - - +
42K GLU* 1.3 64.7 + - - +
44K THR* 3.4 4.3 + - - -
45K ILE* 3.2 30.1 + - + +
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Residues in contact with GLU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K LEU* 3.3 43.1 - - + +
17K LEU* 4.8 5.8 - - + +
18K TYR* 3.3 52.2 + - - +
38K TYR 3.3 15.5 + - - +
39K CYS* 3.3 7.3 + - - +
41K THR* 1.3 79.4 - - - +
43K ARG* 1.3 61.4 + - - +
45K ILE* 3.8 6.6 + - - +
46K ALA* 3.4 21.7 + - - +
53K ARG* 5.3 3.0 + - - +
57K VAL* 5.4 2.1 - - - +
61K LEU* 4.7 16.4 - - + +
68K LEU* 4.0 8.7 - - - +
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Residues in contact with ARG 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLN* 4.0 17.3 + - - +
39K CYS* 2.9 18.1 + - - +
40K TYR* 3.4 37.1 - - - +
41K THR 3.3 0.2 - - - -
42K GLU* 1.3 77.0 - - - +
44K THR* 1.3 62.0 + - - +
46K ALA* 3.5 5.8 + - - +
47K LYS* 2.9 49.8 + - + +
53K ARG* 4.9 19.1 - - - +
61K LEU* 5.2 10.0 - - + +
63K ARG* 5.4 13.4 + - - +
65K CYS 4.1 16.4 + - - -
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Residues in contact with THR 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A U 5.9 2.9 - - - +
205D SER* 3.3 27.8 - - - +
206D GLU* 4.2 15.0 - - + +
40K TYR* 2.7 40.9 + - + -
41K THR* 3.9 3.6 - - - -
42K GLU 3.3 0.4 - - - -
43K ARG* 1.3 79.6 + - - +
45K ILE* 1.3 60.0 + - - +
47K LYS* 3.1 11.6 + - + +
48K ARG* 3.0 28.4 + - - +
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Residues in contact with ILE 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASP* 3.5 33.2 - - - +
205D SER* 3.7 27.8 - - - +
208D SER* 4.8 9.9 - - - +
209D ALA* 6.6 0.2 - - - -
10K ALA* 5.3 7.2 - - + +
13K ARG* 4.6 11.9 - - + +
14K LEU* 5.4 11.2 - - + -
17K LEU* 4.5 2.9 - - + -
41K THR* 3.2 28.7 + - + +
42K GLU* 4.2 4.9 - - - +
43K ARG 3.4 0.2 - - - -
44K THR* 1.3 74.9 - - - +
46K ALA* 1.3 58.6 + - - +
48K ARG* 5.2 1.8 - - - -
49K LEU* 2.9 50.9 + - + +
51K LEU* 6.1 2.2 - - + -
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Residues in contact with ALA 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU* 3.8 21.5 - - + +
42K GLU 3.4 16.3 + - - +
43K ARG 3.7 4.5 - - - +
44K THR 3.3 0.6 - - - -
45K ILE* 1.3 78.5 - - - +
47K LYS* 1.3 60.7 + - - +
49K LEU 3.2 14.6 - - - +
50K VAL* 3.6 10.2 - - - +
51K LEU* 3.8 16.1 + - + +
53K ARG* 4.4 21.8 - - - +
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Residues in contact with LYS 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A C 5.6 10.1 + - - -
121A U 5.7 2.8 + - - -
244A G 6.0 0.9 - - - +
43K ARG* 2.9 38.6 + - + +
44K THR* 3.1 13.4 + - + +
46K ALA* 1.3 79.3 - - - +
48K ARG* 1.3 61.1 + - - +
50K VAL* 3.9 1.6 - - - +
56T C 2.7 69.5 + - - +
57T G 3.4 7.9 - - - +
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Residues in contact with ARG 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 5.4 6.9 - - - +
205D SER 6.0 0.4 - - - +
206D GLU* 2.6 55.8 + - - +
209D ALA* 3.7 19.0 - - + +
210D LYS* 6.0 3.3 - - + +
44K THR 3.0 11.8 + - - +
45K ILE* 4.5 1.8 - - - +
47K LYS* 1.3 74.0 - - - +
49K LEU* 1.3 64.2 + - + +
50K VAL* 3.3 5.9 + - - +
54T U 5.8 1.6 + - - -
55T U 3.8 19.1 + - - -
57T G 3.1 65.2 + - - +
58T A 3.6 11.4 + - - -
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Residues in contact with LEU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D SER* 3.5 32.1 - - - +
209D ALA* 3.9 26.2 - - + +
7K ASP* 5.6 3.1 - - - +
10K ALA* 4.5 21.3 - - + -
45K ILE* 2.9 36.4 + - + +
46K ALA* 3.2 8.3 - - - +
48K ARG* 1.3 72.9 - - + +
50K VAL* 1.3 65.5 + - - +
51K LEU* 3.2 13.4 + - + +
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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) + - + + + + + -
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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