Contacts of the strand formed by residues 4 - 13 (chain C) in PDB entry 3QN3
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 ILE 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 1.3 72.9 - - - +
5C GLU* 1.3 59.9 + - - +
6C ASP 4.1 1.6 - - - +
7C VAL* 3.6 31.0 - - + -
25C VAL* 4.0 11.2 - - + -
26C THR 3.9 3.6 - - - -
27C LEU* 4.1 15.3 - - + -
78C ILE* 3.7 34.5 - - + +
79C LEU* 3.7 8.9 - - + +
80C GLY* 2.8 26.7 + - - -
81C LEU* 3.0 19.1 + - + +
82C ASP 5.0 1.6 - - - +
83C ALA* 4.5 5.4 - - - -
89C LEU* 4.3 13.0 - - + -
117C THR* 3.9 25.6 - - + +
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Residues in contact with GLU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 3.3 3.0 + - + -
4C ILE* 1.3 71.2 - - - +
6C ASP* 1.3 61.9 + - + +
26C THR* 2.7 20.7 + - + +
27C LEU 3.9 13.9 - - - +
28C SER* 3.5 27.3 - - - +
30C GLY 5.4 0.2 + - - -
79C LEU* 3.2 20.2 - - - +
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Residues in contact with ASP 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 1.3 85.5 - - + +
7C VAL* 1.3 73.9 + - - +
8C ARG* 4.2 23.3 - - - +
24C GLU* 4.0 3.0 - - - +
25C VAL* 3.2 5.0 - - - +
26C THR* 2.8 51.6 + - + +
79C LEU* 3.4 7.6 - - - +
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.6 14.6 - - + -
6C ASP* 1.3 88.6 + - - +
8C ARG* 1.3 69.0 + - - +
23C ALA* 5.7 0.2 - - + -
24C GLU 3.5 7.6 - - - +
25C VAL* 4.2 9.2 - - + -
70C VAL* 3.6 25.8 - - + +
71C ASN* 4.1 6.1 - - - +
74C ILE* 4.8 1.8 - - + -
75C ALA* 4.2 23.7 - - + +
78C ILE* 3.4 33.7 - - + -
79C LEU* 4.1 8.4 - - + +
113C VAL* 3.9 17.3 - - + -
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Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP* 4.2 14.1 - - - +
7C VAL* 1.3 77.8 - - - +
9C ALA* 1.3 65.7 + - - +
10C TYR* 3.8 31.8 - - + +
23C ALA* 3.3 4.3 - - - +
24C GLU* 2.8 69.9 + - + +
70C VAL* 3.8 5.7 - - - +
71C ASN* 3.1 13.4 - - - +
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 1.3 80.8 + - - +
10C TYR* 1.3 71.3 + - - +
21C VAL* 3.8 17.3 - - + -
22C LYS 3.1 16.2 - - - +
23C ALA* 4.3 1.3 - - - -
67C VAL* 3.7 12.5 - - + +
70C VAL* 3.7 25.8 - - + -
71C ASN* 2.8 24.2 + - - +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ARG* 3.8 36.3 - - - +
9C ALA* 1.3 81.2 - - - +
11C GLU* 1.3 65.1 + - - +
12C VAL* 3.8 25.4 - - + -
21C VAL* 3.9 0.3 - - - -
22C LYS* 3.0 67.5 + - + +
24C GLU* 4.4 21.4 + - + +
34C ALA* 5.5 0.2 - - - +
67C VAL* 3.6 15.9 - - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TYR* 1.3 78.0 - - - +
12C VAL* 1.3 67.9 + - - +
19C PRO* 3.8 9.4 - - + +
20C THR 3.5 5.2 - - - -
57C ARG* 2.7 38.4 + - - -
58C PHE* 4.1 5.9 - - - -
62C GLY* 3.5 3.8 - - - -
63C VAL* 3.1 40.1 + - + -
64C LEU* 3.5 27.2 + - + +
67C VAL* 3.9 3.9 - - + +
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TYR* 3.7 26.4 + - + -
11C GLU* 1.3 80.0 - - - +
13C LEU* 1.3 68.4 + - - +
19C PRO* 3.1 8.7 - - - +
20C THR* 2.9 51.1 + - + +
22C LYS* 3.9 21.1 - - + +
36C ILE* 3.8 23.3 - - + -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 1.3 88.2 - - - +
14C ASP* 1.3 67.2 + - - +
17C GLY* 4.0 27.6 - - - +
18C ASN 3.4 5.8 - - - +
19C PRO* 4.4 0.9 - - + -
20C THR* 4.5 4.6 - - - +
36C ILE* 5.4 0.5 - - - +
58C PHE* 4.2 24.0 - - + -
365C SER* 5.0 2.8 - - - -
366C GLU* 4.8 9.9 - - - +
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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