Contacts of the strand formed by residues 36 - 42 (chain A) in PDB entry 3Q2K
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 ALA 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.9 3.3 - - - +
11A ILE* 3.3 9.4 - - + +
13A PHE* 4.0 26.9 - - + -
29A ILE* 4.3 11.6 - - + +
32A HIS 3.3 7.8 + - - +
33A GLY* 3.2 24.9 - - - +
34A ASP 3.6 0.6 - - - -
35A ARG* 1.3 81.0 - - - +
37A GLU* 1.3 68.5 + - - +
309A ILE* 4.1 15.7 - - + -
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Residues in contact with GLU 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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10A LYS* 4.2 23.9 - - + +
11A ILE 2.8 14.9 + - - +
12A ARG* 3.8 10.0 - - + +
13A PHE* 3.0 26.5 + - - +
29A ILE* 3.9 10.1 - - - -
33A GLY 5.4 0.2 - - - +
36A ALA* 1.3 79.7 - - - +
38A LEU* 1.3 64.0 + - - +
39A VAL* 3.2 28.1 + - + +
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Residues in contact with LEU 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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13A PHE* 3.7 20.0 - - + +
15A LEU* 4.1 18.6 - - + +
26A ILE* 3.8 36.6 - - + -
29A ILE* 3.8 27.8 - - + +
37A GLU* 1.3 77.1 - - - +
39A VAL* 1.3 58.6 + - - +
40A GLU 3.8 12.3 - - - +
41A ILE* 4.2 16.4 - - + -
56A THR* 4.0 22.9 - - + +
58A ALA* 3.5 14.4 - - + +
77A VAL* 6.3 0.2 - - + -
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Residues in contact with VAL 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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12A ARG* 3.6 38.8 - - + -
13A PHE 2.9 10.4 + - - +
37A GLU* 3.2 25.8 + - - +
38A LEU* 1.3 73.9 - - - +
40A GLU* 1.3 79.5 + - + +
58A ALA* 3.2 5.0 - - - +
59A ARG* 3.0 24.8 + - + +
72A ASN* 4.8 7.6 - - - +
73A ALA* 5.8 1.6 - - + -
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE 3.4 3.0 + - - -
14A GLY* 3.0 10.2 - - - -
15A LEU 2.9 23.3 + - - -
38A LEU* 3.7 3.0 - - - +
39A VAL* 1.3 93.1 - - + +
41A ILE* 1.3 70.3 + - - +
58A ALA* 4.2 0.2 - - - -
59A ARG* 3.6 11.8 + - + +
61A PHE* 3.8 18.2 - - + -
67A MET* 4.1 16.2 - - - +
71A GLY* 3.2 18.5 - - - -
72A ASN* 2.8 33.5 + - - -
73A ALA* 3.4 25.9 + - - +
76A LEU* 5.1 0.2 - - - +
97A ARG* 5.1 0.9 + - - -
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Residues in contact with ILE 41 (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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15A LEU* 3.2 19.7 - - + +
18A CYS* 4.2 8.3 - - - -
26A ILE* 6.2 0.2 - - + -
38A LEU* 4.2 19.1 - - + -
40A GLU* 1.3 81.4 - - - +
42A CYS* 1.3 62.2 + - - +
49A LEU* 3.8 17.5 - - + -
52A ALA* 3.8 12.3 - - + +
53A GLU* 3.6 39.7 - - + +
56A THR* 4.1 6.5 - - + +
58A ALA* 4.2 14.8 - - + +
59A ARG 3.0 14.5 + - - +
60A PRO* 3.9 0.7 - - + -
61A PHE* 3.1 27.7 + - - +
67A MET* 4.1 2.2 - - - -
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Residues in contact with CYS 42 (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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15A LEU 3.0 8.6 + - - +
16A VAL* 4.2 7.4 - - - -
17A GLY* 3.0 26.5 + - - -
18A CYS* 3.8 3.2 - - - -
41A ILE* 1.3 78.1 - - - +
43A ASP* 1.3 68.6 + - - +
49A LEU* 4.1 2.0 - - - -
61A PHE* 3.3 10.1 - - + +
62A SER 4.5 0.2 - - - -
63A SER* 3.4 12.1 - - - -
64A LEU* 3.4 33.7 - - - -
67A MET* 3.6 21.8 - - + -
500A NAI 4.1 16.9 + - - -
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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