Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 6E8Y
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 PHE 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.8 4.3 - - - -
4A LYS* 3.6 16.4 - - + +
6A VAL* 4.5 4.3 - - + -
25A ASN 4.3 2.0 - - - -
26A ALA* 3.8 22.4 - - + +
29A LEU* 3.3 21.2 + - + +
30A ALA 3.1 5.1 - - - +
31A GLN* 1.3 104.7 - - + +
33A ASP* 1.3 59.8 + - - +
34A PRO* 3.4 1.4 - - - +
88A ILE* 4.2 13.0 - - + -
176A LEU* 3.4 51.6 - - + -
179A GLU 4.1 0.4 - - - -
180A LEU* 3.8 42.2 - - + -
403A K 2.7 27.5 - - - -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 3.5 21.0 + - - +
4A LYS 2.9 18.0 + - - +
5A LYS* 3.8 35.8 + - + -
6A VAL* 5.3 2.6 + - - +
26A ALA* 3.7 12.0 - - - +
32A PHE* 1.3 71.6 - - - +
34A PRO* 1.3 73.2 - - - +
35A ARG* 2.7 47.3 + - - +
36A VAL* 4.1 1.4 - - - +
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Residues in contact with PRO 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 3.9 11.4 - - - +
27A ALA* 3.9 21.8 - - + +
32A PHE 3.5 7.4 - - - +
33A ASP* 1.3 91.1 - - - +
35A ARG* 1.3 56.9 + - + +
36A VAL* 3.0 8.6 + - - +
72A ASN* 2.9 34.3 + - + +
403A K 3.6 7.2 - - - -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.1 18.9 - - + +
6A VAL 4.2 8.7 + - - +
33A ASP* 2.7 31.9 + - - +
34A PRO* 1.3 71.8 - - + +
36A VAL* 1.3 61.5 + - - +
37A THR* 3.3 31.2 + - - +
72A ASN* 3.8 5.2 - - - +
74A VAL* 4.4 24.1 - - + +
76A VAL* 5.1 5.5 - - - +
81A GLN 5.3 4.8 + - - -
85A ASP* 5.6 6.9 + - - +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.5 24.5 - - + +
8A ILE* 3.8 27.1 - - + -
22A VAL* 4.3 8.3 - - + +
23A GLY* 4.5 1.3 - - - -
26A ALA* 3.4 32.5 - - + -
33A ASP 4.1 2.2 - - - +
34A PRO 3.0 9.3 + - - +
35A ARG* 1.3 75.1 - - - +
37A THR* 1.3 75.0 + - - +
72A ASN* 3.2 9.9 + - - +
73A VAL* 3.3 15.3 - - + +
74A VAL* 3.0 24.9 + - - +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL 3.2 6.6 + - - -
7A CYS* 3.2 16.2 - - - +
8A ILE 2.8 24.7 + - - -
35A ARG* 3.3 42.0 + - + +
36A VAL* 1.3 79.4 - - - +
38A MET* 1.3 62.7 + - - +
39A TRP 4.2 0.2 - - - -
74A VAL* 3.6 7.4 - - + +
76A VAL* 4.3 12.1 - - + -
81A GLN 5.1 0.2 - - - +
82A ALA* 2.8 36.1 + - - +
86A ALA* 5.1 0.5 - - - +
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Residues in contact with MET 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.3 12.6 - - + +
10A GLY 3.0 13.2 - - - +
11A SER* 2.5 56.3 - - - -
15A GLY 4.1 7.4 - - - +
16A SER* 4.1 11.7 - - - +
19A ALA* 3.9 24.9 - - - -
37A THR* 1.3 76.8 - - - +
39A TRP* 1.3 60.2 + - - +
40A VAL* 3.8 5.8 - - + +
54A ILE* 5.4 4.3 - - + -
60A ASN* 4.7 2.7 - - - +
69A LEU* 5.0 8.1 - - + -
73A VAL* 4.0 17.5 - - + -
74A VAL 2.9 11.9 + - - +
75A ALA* 3.3 6.0 - - - -
76A VAL 3.0 22.5 + - - -
82A ALA* 4.7 2.5 - - - -
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Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A CYS* 5.2 0.2 - - - -
8A ILE 2.9 13.7 + - - +
9A VAL* 4.2 8.7 - - + -
10A GLY* 3.5 28.7 - - - -
11A SER* 3.3 13.0 + - - -
37A THR 4.2 0.2 - - - -
38A MET* 1.3 70.5 - - - +
40A VAL* 1.3 60.5 + - - +
41A PHE* 3.9 40.4 - + + -
76A VAL 3.3 19.1 - - - -
77A PRO 2.9 18.4 + - - -
79A VAL* 3.3 45.1 - - + +
82A ALA* 4.0 16.1 - - + +
93A VAL* 3.9 8.7 - - + -
97A PHE* 5.9 4.0 - + + -
101A ILE* 3.5 35.2 - - + -
104A GLN* 5.3 3.8 - - - -
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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
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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