Contacts of the strand formed by residues 2 - 10 (chain D) in PDB entry 3B13
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 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 1.3 81.7 - - - +
3D ALA* 1.3 70.7 + - - +
4D ILE* 4.5 4.6 - - + +
49D LYS* 5.0 6.4 - - - +
50D PRO 3.3 10.0 + - - +
51D VAL* 3.1 11.6 - - + +
52D ASN* 3.0 21.0 + - - -
176D VAL* 4.3 20.8 + - - +
177D LEU* 2.9 36.8 + - - +
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Residues in contact with ALA 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523C PRO* 5.4 16.4 - - + -
1525C ASN* 6.1 5.6 - - + +
1526C PRO* 5.9 7.0 - - + -
2D GLN* 1.3 80.4 + - - +
4D ILE* 1.3 66.9 + - - +
5D LYS 4.4 0.2 - - - -
52D ASN* 3.5 16.2 - - + +
76D ASP* 4.1 8.6 - - - +
176D VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 4.3 7.6 - - + +
3D ALA* 1.3 81.8 - - - +
5D LYS* 1.3 61.7 + - - +
51D VAL* 4.1 13.7 - - + -
52D ASN 2.9 11.5 + - - +
53D LEU* 3.4 24.0 - - + -
54D GLY 2.9 29.8 + - - +
76D ASP* 3.6 15.5 - - + -
77D VAL* 4.3 9.4 - - + -
173D ILE* 3.5 36.6 - - + -
176D VAL* 4.1 31.9 - - + -
177D LEU* 4.5 6.5 - - + -
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Residues in contact with LYS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525C ASN* 4.0 28.1 + - + +
1595C LEU* 4.2 7.5 - - - +
3D ALA 4.4 0.2 - - - -
4D ILE* 1.3 70.5 - - - +
6D CYS* 1.3 60.5 + - - +
7D VAL* 4.0 5.4 - - + -
54D GLY* 4.0 2.9 - - - +
56D TRP* 3.4 50.9 - - + +
71D SER 2.7 28.3 + - - -
73D PRO 3.1 14.5 + - - -
74D GLN 3.4 19.7 - - - +
75D THR* 3.3 18.6 - - - +
76D ASP* 2.8 40.4 + - - +
77D VAL 3.3 6.2 + - - -
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Residues in contact with CYS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE 3.7 0.2 + - - -
5D LYS* 1.3 75.3 - - - +
7D VAL* 1.3 62.0 + - - +
8D VAL* 4.1 0.4 + - - -
53D LEU* 3.9 14.1 - - + -
54D GLY 2.9 10.2 + - - +
55D LEU* 3.4 30.3 - - + +
56D TRP* 2.9 26.0 + - - +
77D VAL* 3.3 26.0 - - + +
79D LEU* 3.7 33.2 - - - -
169D PHE* 5.8 0.2 - - - -
172D ALA* 4.5 5.2 - - - -
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 4.0 17.0 - - - -
6D CYS* 1.3 75.3 - - - +
8D VAL* 1.3 64.5 + - - +
9D VAL* 4.3 2.2 - - + -
56D TRP* 3.7 12.1 - - + +
58D THR* 3.7 27.1 - - + -
71D SER* 4.8 5.8 - - - +
72D TYR* 4.1 9.9 - - + -
75D THR* 3.1 30.7 - - + +
77D VAL 3.1 7.1 + - - -
78D PHE* 3.5 28.9 - - + -
79D LEU 2.9 23.9 + - - +
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D CYS* 4.6 4.5 - - - +
7D VAL* 1.3 76.2 - - - +
9D VAL* 1.3 58.3 + - - +
16D LYS* 3.7 31.5 - - + +
19D LEU* 5.5 1.1 - - + -
20D LEU* 3.7 32.5 - - + -
55D LEU* 4.7 4.5 - - + -
56D TRP 2.8 19.6 + - - +
57D ASP* 4.5 1.6 - - - -
58D THR* 2.6 34.7 + - - -
79D LEU* 3.6 20.6 - - + +
81D CYS* 3.8 22.2 - - - -
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 4.3 6.7 - - + -
8D VAL* 1.3 77.9 - - - +
10D GLY* 1.3 58.7 + - - +
16D LYS* 3.9 5.8 - - - +
58D THR* 3.4 20.6 - - + +
68D ARG* 4.9 0.4 - - - -
72D TYR* 3.5 27.1 - - + +
78D PHE* 4.7 4.5 - - + -
79D LEU 3.0 17.2 + - - +
80D ILE* 3.8 22.0 - - + -
81D CYS* 2.9 30.3 + - - +
97D TRP* 4.1 20.2 - - + -
101D VAL* 4.1 15.7 - - + -
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Residues in contact with GLY 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 1.3 76.6 - - - +
11D ASP* 1.3 69.4 + - - +
14D VAL* 4.4 0.9 - - - -
16D LYS* 3.2 18.4 + - - +
60D GLY* 3.5 5.0 - - - -
81D CYS 3.4 15.7 - - - -
97D TRP* 3.3 32.6 - - - -
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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