Contacts of the helix formed by residues 18 - 34 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J TYR* 2.9 38.0 + - + +
16J GLN* 4.3 17.1 - - + +
17J GLN* 1.3 73.2 - - - +
19J TYR* 1.3 59.4 + - - +
20J GLN 3.5 1.8 - - - -
21J SER* 4.0 7.2 - - - -
22J ALA* 3.1 26.7 + - - +
74K TYR* 3.5 17.5 + - - -
78K ARG* 4.3 2.5 + - - +
131K SER* 3.3 26.2 - - - +
134K LEU* 3.0 31.6 - - - +
138K LYS* 5.0 3.2 + - - +
163K CYS* 4.9 4.9 - - + -
165K GLU* 3.9 17.3 + - - +
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Residues in contact with TYR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 3.8 27.8 + - + -
17J GLN* 3.0 44.6 + - + +
18J GLN* 1.3 70.3 - - - +
20J GLN* 1.3 62.2 + - + +
22J ALA* 3.2 3.5 + - - +
23J LEU* 2.8 32.7 + - - +
46J CYS* 4.5 1.9 - - - -
49J LEU* 3.1 61.4 - - + +
50J THR* 4.7 12.9 + - + +
19K TYR* 4.5 10.0 + - - -
48K TYR* 6.4 0.9 - + - -
49K LEU* 5.3 3.8 - - - +
78K ARG* 5.2 3.8 - - - -
165K GLU* 3.9 2.6 + - - -
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Residues in contact with GLN 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLN 3.5 0.2 - - - -
19J TYR* 1.3 79.9 - - - +
21J SER* 1.3 58.1 + - - +
23J LEU* 3.5 8.9 + - - +
24J PHE* 3.2 21.3 + - - +
50J THR* 4.5 7.1 - - + +
164K PHE* 4.7 11.1 - - - -
165K GLU* 3.2 34.6 + - + +
168K ASP* 4.7 13.3 + - - +
265K LYS* 2.8 36.5 + - - +
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Residues in contact with SER 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J TYR* 3.5 26.0 - - - -
18J GLN* 3.6 16.5 + - - -
19J TYR 3.2 0.2 - - - -
20J GLN* 1.3 77.5 - - - +
22J ALA* 1.3 65.3 + - - +
24J PHE* 3.3 6.4 + - - +
25J TRP* 3.2 27.6 + - - -
163K CYS* 3.7 3.4 - - - -
164K PHE* 3.7 13.3 + - - +
165K GLU* 3.2 31.9 - - - +
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Residues in contact with ALA 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J VAL* 3.4 13.1 - - + +
13J TYR* 3.6 23.5 - - + +
14J LEU* 3.9 14.4 - - + -
18J GLN 3.1 18.8 + - - +
19J TYR 3.2 4.0 + - - +
21J SER* 1.3 76.9 + - - +
23J LEU* 1.3 52.6 + - - +
25J TRP* 3.2 2.2 + - - -
26J ALA* 2.7 37.4 + - - +
46J CYS* 3.7 16.4 - - - -
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J TYR 2.8 17.5 + - - +
20J GLN* 3.6 10.8 - - - +
21J SER 3.2 0.2 - - - -
22J ALA* 1.3 76.5 - - - +
24J PHE* 1.3 63.4 + - - +
26J ALA* 3.2 1.0 + - - +
27J ASP* 3.0 24.3 + - + +
43J LEU* 3.7 20.4 - - + -
46J CYS* 3.5 15.9 - - + -
47J LEU* 3.7 33.2 - - + -
50J THR* 4.0 12.8 - - - +
55J ARG* 4.0 14.1 - - - +
265K LYS* 3.3 31.4 - - + +
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Residues in contact with PHE 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J GLN 3.2 6.7 + - - +
21J SER 3.5 7.2 - - - +
22J ALA 3.3 0.2 - - - -
23J LEU* 1.3 82.8 - - - +
25J TRP* 1.3 100.6 + + - +
27J ASP* 3.6 7.0 + - - +
28J LYS* 3.2 58.4 + - + +
164K PHE* 3.5 62.8 - + + -
204K LEU* 4.3 15.7 - - + -
205K PHE* 5.0 4.3 - + - -
208K LYS* 4.4 6.7 - - - -
232K ASP* 4.3 13.0 - - - -
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Residues in contact with TRP 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J LEU* 3.4 41.5 - - + -
9J ARG* 6.1 1.6 - - + -
10J VAL* 4.6 14.4 - - + +
13J TYR* 4.7 10.1 - + + -
21J SER* 3.2 22.5 + - - +
22J ALA* 3.9 5.6 - - - +
24J PHE* 1.3 98.5 - + - +
26J ALA* 1.3 60.2 + - - +
27J ASP 3.2 0.4 - - - -
28J LYS* 3.2 15.9 + - + +
29J VAL* 2.8 33.7 + - - +
32J LEU* 5.5 0.4 - - + -
162K TYR* 3.0 38.7 + + - -
164K PHE* 4.8 0.2 - - + -
200K LEU* 4.3 11.4 - - + -
201K LEU* 3.5 34.1 - - + -
204K LEU* 3.6 22.4 - - + -
205K PHE* 5.3 2.2 - + - -
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Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J VAL* 3.8 17.7 - - + +
22J ALA 2.7 22.6 + - - +
23J LEU* 3.2 5.8 + - - +
25J TRP* 1.3 72.7 - - - +
27J ASP* 1.3 63.7 + - - +
29J VAL* 3.4 9.6 + - - +
30J ALA* 3.2 20.8 + - - +
39J ASP 4.9 2.4 - - - +
42J TRP* 4.5 3.4 - - + +
43J LEU* 4.1 26.0 - - + +
46J CYS* 4.0 14.6 - - + -
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Residues in contact with ASP 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J LEU* 3.0 17.6 + - + +
24J PHE* 3.7 7.4 - - - +
26J ALA* 1.3 75.1 - - - +
28J LYS* 1.3 64.8 + - - +
30J ALA* 3.3 4.7 + - - +
31J SER* 3.2 22.3 + - - -
43J LEU* 4.1 29.0 - - + +
55J ARG* 4.9 8.3 + - - -
230K ASN* 3.8 17.5 + - - +
231K LEU* 5.3 3.3 + - - +
232K ASP* 3.9 15.0 - - - +
264K HIS* 4.0 14.9 + - - -
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Residues in contact with LYS 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PHE* 3.2 45.8 - - + +
25J TRP* 3.2 29.9 + - + +
27J ASP* 1.3 74.9 - - - +
29J VAL* 1.3 56.8 + - - +
31J SER* 3.1 1.6 + - - -
32J LEU* 2.7 42.7 + - + +
204K LEU* 3.5 27.9 - - + +
208K LYS* 4.4 3.2 - - - +
227K LEU* 4.0 17.7 - - + +
230K ASN* 3.3 24.8 - - - +
232K ASP* 3.1 33.2 + - - +
233K VAL* 4.9 2.6 - - - +
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Residues in contact with VAL 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J LEU* 5.5 1.6 - - + +
6J LEU* 4.0 44.8 - - + +
7J ARG* 4.3 13.9 - - + +
10J VAL* 4.5 10.8 - - + -
25J TRP 2.8 19.7 + - - +
26J ALA* 3.4 11.9 - - - +
27J ASP 3.3 0.2 - - - -
28J LYS* 1.3 77.1 - - - +
30J ALA* 1.3 57.7 + - - +
32J LEU* 4.1 3.8 - - - +
33J SER* 2.9 32.0 + - - -
39J ASP* 3.8 30.5 - - + +
42J TRP* 6.3 3.1 - - + -
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ALA 3.2 9.0 + - - +
27J ASP* 3.5 11.0 - - - +
29J VAL* 1.3 80.5 - - - +
31J SER* 1.3 59.3 + - - +
34J ARG 2.9 36.2 + - - +
35J GLU* 3.5 7.9 + - + -
39J ASP* 4.5 18.4 - - - +
40J ILE* 4.9 14.4 - - + -
43J LEU* 4.5 15.9 - - + -
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ASP* 3.2 13.7 + - - -
28J LYS 3.1 4.9 + - - -
30J ALA* 1.3 80.9 - - - +
32J LEU* 1.3 61.2 + - - +
34J ARG* 3.4 15.0 + - - +
35J GLU* 5.4 1.1 - - - +
226K GLY* 3.9 17.5 - - - +
227K LEU* 4.6 4.7 - - - -
229K LYS* 4.7 1.9 - - - +
230K ASN* 3.4 45.5 + - - +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 6.1 3.6 - - + -
6J LEU* 3.7 29.4 - - + -
25J TRP* 5.5 0.4 - - + -
28J LYS* 2.7 24.7 + - + +
29J VAL* 4.1 3.4 - - - +
31J SER* 1.3 73.7 - - - +
33J SER* 1.3 61.5 + - - +
34J ARG* 3.4 5.9 + - - +
200K LEU* 4.2 17.7 - - + -
225K ASP* 3.7 38.8 - - + +
226K GLY* 4.2 8.5 + - - +
227K LEU* 3.7 23.8 - - + +
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Residues in contact with SER 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J LEU* 5.0 9.6 - - - +
7J ARG* 3.3 18.1 + - - -
29J VAL* 2.9 20.8 + - - -
32J LEU* 1.3 76.0 - - - +
34J ARG* 1.3 73.7 + - - +
36J GLU* 3.9 11.3 + - - +
39J ASP* 2.6 29.4 + - - -
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Residues in contact with ARG 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ALA* 2.9 15.9 + - - +
31J SER* 3.4 9.1 + - - +
32J LEU 3.2 7.7 + - - +
33J SER* 1.3 89.9 - - - +
35J GLU* 1.3 71.3 + - - +
36J GLU* 3.1 10.2 + - - +
39J ASP* 4.3 0.5 - - - +
225K ASP 5.2 1.2 - - - -
226K GLY* 4.1 24.5 + - - +
229K LYS* 3.4 38.2 - - - +
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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