Contacts of the helix formed by residues 18 - 34 (chain K) in PDB entry 5A31
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 18 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J TYR* 3.6 17.0 + - - -
78J ARG* 4.4 1.8 + - - +
131J SER* 3.3 26.9 - - - +
134J LEU* 3.1 22.9 - - - +
138J LYS* 5.1 1.6 - - - +
163J CYS* 4.9 5.0 - - + -
165J GLU* 2.6 33.8 + - - +
13K TYR* 2.9 39.9 + - + +
16K GLN* 4.4 15.7 - - + +
17K GLN* 1.3 71.9 - - - +
19K TYR* 1.3 59.0 + - - +
20K GLN 3.5 1.6 - - - -
21K SER* 4.0 6.3 - - - -
22K ALA* 3.1 26.3 + - - +
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Residues in contact with TYR 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J TYR* 4.5 9.5 + - - -
48J TYR* 6.4 0.7 - + - -
49J LEU* 5.2 3.6 - - - +
78J ARG* 5.2 4.3 - - - -
165J GLU* 4.5 2.2 + - - -
14K LEU* 3.8 27.1 - - + -
17K GLN* 3.0 45.8 + - + +
18K GLN* 1.3 69.8 - - - +
20K GLN* 1.3 61.6 + - + +
22K ALA* 3.2 3.6 + - - +
23K LEU* 2.8 33.0 + - - +
46K CYS* 4.5 1.9 - - - -
49K LEU* 3.0 64.2 - - + +
50K THR* 4.7 13.6 + - + +
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Residues in contact with GLN 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J PHE* 4.6 12.8 - - - -
165J GLU* 3.2 32.5 + - + +
168J ASP* 5.0 5.7 + - - +
18K GLN 3.5 0.2 - - - -
19K TYR* 1.3 79.5 - - + +
21K SER* 1.3 58.7 + - - +
23K LEU* 3.5 13.9 + - - +
24K PHE* 3.2 20.1 + - - +
50K THR* 4.2 20.4 - - + +
52K GLN* 4.7 4.0 + - - +
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Residues in contact with SER 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J CYS* 3.7 13.8 - - - -
164J PHE* 3.7 3.4 + - - +
165J GLU* 3.8 30.6 - - - +
13K TYR* 3.5 24.6 - - - -
18K GLN* 3.6 19.2 + - - -
19K TYR 3.2 0.6 - - - -
20K GLN* 1.3 76.2 - - - +
22K ALA* 1.3 64.5 + - - +
24K PHE* 3.3 7.1 + - - +
25K TRP* 3.2 26.9 + - - -
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Residues in contact with ALA 22 (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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10K VAL* 3.4 12.7 - - + +
13K TYR* 3.6 23.1 - - + +
14K LEU* 3.9 14.4 - - + -
18K GLN 3.1 19.8 + - - +
19K TYR 3.7 3.1 - - - +
21K SER* 1.3 77.1 + - - +
23K LEU* 1.3 53.7 + - - +
25K TRP* 3.2 1.6 + - - -
26K ALA* 2.6 37.9 + - - +
46K CYS* 3.7 15.7 - - - -
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Residues in contact with LEU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K TYR 2.8 17.9 + - - +
20K GLN* 3.6 16.4 - - - +
22K ALA* 1.3 77.2 - - - +
24K PHE* 1.3 64.3 + - - +
26K ALA* 3.5 0.4 - - - +
27K ASP* 3.0 24.3 + - + +
43K LEU* 3.7 20.9 - - + -
46K CYS* 3.5 17.4 - - + -
47K LEU* 3.6 35.4 - - + -
50K THR* 3.8 25.1 - - + +
52K GLN* 4.1 6.7 - - - +
55K ARG* 4.0 14.4 - - - +
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Residues in contact with PHE 24 (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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164J PHE* 3.5 63.9 - + + -
204J LEU* 4.2 16.6 - - + -
205J PHE* 5.0 2.9 - + - -
208J LYS* 4.0 9.6 - - - -
232J ASP* 4.2 8.3 - - - -
20K GLN* 3.2 6.3 + - - +
21K SER 3.5 6.3 - - - +
22K ALA 3.3 0.2 - - - -
23K LEU* 1.3 82.4 - - - +
25K TRP* 1.3 101.7 + + - +
27K ASP* 3.6 6.2 + - - +
28K LYS* 3.2 57.6 + - + +
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Residues in contact with TRP 25 (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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162J TYR* 2.9 38.2 + + - -
164J PHE* 4.4 1.0 - - + +
200J LEU* 4.5 12.1 - - + -
201J LEU* 3.4 34.5 - - + -
204J LEU* 3.7 20.6 - - + -
205J PHE* 5.2 2.9 - + - -
6K LEU* 3.4 41.1 - - + -
9K ARG* 6.1 0.7 - - + -
10K VAL* 4.6 14.4 - - + +
13K TYR* 4.7 10.5 - + + -
21K SER* 3.2 21.6 + - - +
22K ALA* 4.0 5.2 - - - +
24K PHE* 1.3 97.2 - + - +
26K ALA* 1.3 54.6 + - - +
28K LYS* 3.2 15.7 + - + +
29K VAL* 2.8 39.2 + - - +
32K LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 26 (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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10K VAL* 3.8 18.5 - - + +
22K ALA 2.6 22.1 + - - +
23K LEU* 3.5 5.6 - - - +
25K TRP* 1.3 72.0 - - - +
27K ASP* 1.3 61.6 + - - +
29K VAL* 3.4 8.4 + - - +
30K ALA* 3.2 21.8 + - - +
39K ASP 4.9 2.6 - - - +
42K TRP* 4.5 4.0 - - + +
43K LEU* 4.1 26.4 - - + +
46K CYS* 4.0 14.4 - - + -
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Residues in contact with ASP 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230J ASN* 3.8 15.3 + - - +
231J LEU* 5.6 1.6 - - - +
232J ASP* 3.8 20.2 - - - +
264J HIS* 4.2 15.9 - - - -
23K LEU* 3.0 17.1 + - + +
24K PHE* 3.7 7.2 - - - +
26K ALA* 1.3 74.9 - - - +
28K LYS* 1.3 64.5 + - - +
30K ALA* 3.3 5.2 + - - +
31K SER* 3.2 22.2 + - - -
43K LEU* 4.1 29.2 - - + +
55K ARG* 4.9 8.0 + - - -
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Residues in contact with LYS 28 (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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200J LEU* 6.4 0.2 - - + -
204J LEU* 3.4 36.1 - - + +
207J ASN* 5.2 0.4 - - - +
208J LYS* 4.6 3.6 - - - +
227J LEU* 4.4 14.1 - - + +
230J ASN* 3.6 21.0 - - - +
232J ASP* 3.3 40.3 - - - +
233J VAL* 4.7 4.4 - - - +
24K PHE* 3.2 37.7 - - + +
25K TRP* 3.2 28.2 + - + +
27K ASP* 1.3 73.3 - - - +
29K VAL* 1.3 56.5 + - - +
31K SER* 3.1 1.7 + - - -
32K LEU* 2.7 42.3 + - + +
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Residues in contact with VAL 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 5.7 1.1 - - + +
6K LEU* 4.0 43.9 - - + +
7K ARG* 4.3 13.9 - - + +
10K VAL* 4.5 11.4 - - + -
25K TRP 2.8 26.1 + - - +
26K ALA* 3.4 8.3 - - - +
28K LYS* 1.3 71.8 - - - +
30K ALA* 1.3 57.6 - - - +
32K LEU* 4.6 4.5 - - - +
33K SER* 2.9 31.5 + - - -
39K ASP* 3.8 30.7 - - + +
42K TRP* 6.3 2.7 - - + -
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Residues in contact with ALA 30 (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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26K ALA 3.2 9.9 + - - +
27K ASP* 3.5 11.0 - - - +
28K LYS 3.2 0.2 - - - -
29K VAL* 1.3 81.8 - - - +
31K SER* 1.3 58.8 + - - +
34K ARG 2.9 36.8 + - - +
35K GLU* 3.5 7.3 + - + -
39K ASP* 4.4 17.3 - - - +
40K ILE* 4.9 14.4 - - + -
43K LEU* 4.5 16.2 - - + -
63K ARG* 5.6 0.9 - - - +
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Residues in contact with SER 31 (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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226J GLY 4.7 10.6 - - - +
227J LEU* 4.3 9.9 - - - -
229J LYS 4.8 0.5 - - - -
230J ASN* 3.5 50.3 + - - +
27K ASP* 3.2 7.7 + - - -
28K LYS 3.1 3.6 + - - -
30K ALA* 1.3 78.5 - - - +
32K LEU* 1.3 63.3 + - - +
34K ARG* 3.4 13.1 + - - +
35K GLU* 5.4 0.7 - - - +
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Residues in contact with LEU 32 (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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200J LEU* 4.2 18.4 - - + -
224J VAL* 4.2 13.0 - - + -
225J ASN* 6.4 0.4 - - + -
226J GLY* 5.3 6.4 - - - +
227J LEU* 3.7 37.0 - - + +
3K LEU* 6.2 2.9 - - + -
6K LEU* 3.7 29.6 - - + -
25K TRP* 5.5 0.2 - - + -
28K LYS* 2.7 25.1 + - + +
29K VAL* 4.1 3.6 - - - +
31K SER* 1.3 73.4 - - - +
33K SER* 1.3 63.3 - - - +
34K ARG* 3.3 4.0 + - - +
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Residues in contact with SER 33 (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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3K LEU* 5.0 9.1 - - - +
7K ARG* 3.3 18.2 + - - -
29K VAL* 2.9 16.6 + - - -
32K LEU* 1.3 76.8 - - - +
34K ARG* 1.3 75.3 + - - +
36K GLU* 4.0 13.3 + - - +
39K ASP* 2.6 29.7 + - - -
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Residues in contact with ARG 34 (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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30K ALA* 2.9 16.4 + - - +
31K SER* 3.4 9.5 + - - +
32K LEU 3.2 5.8 - - - +
33K SER* 1.3 89.6 - - - +
35K GLU* 1.3 72.1 + - - +
36K GLU* 3.1 10.0 + - - +
39K ASP* 4.3 0.7 - - - +
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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
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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