Contacts of the helix formed by residues 63 - 72 (chain A) 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 VAL 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 2.9 26.1 + - + -
19A PRO* 4.1 3.6 - - + +
20A THR* 3.4 36.3 - - - +
21A VAL* 3.8 13.5 - - + -
51A LEU 3.7 8.1 - - - +
52A ARG* 3.5 28.9 - - - +
53A ASP* 3.9 2.2 - - - -
61A LYS 3.9 0.4 - - - +
62A GLY* 1.3 73.9 - - - +
64A LEU* 1.3 63.6 + - - +
65A LYS 3.3 2.7 - - - -
66A ALA* 3.3 3.1 + - + -
67A VAL* 3.0 24.1 + - + +
108A ASN* 3.7 22.7 - - - +
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Residues in contact with LEU 64 (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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11A GLU* 3.5 27.4 - - + +
53A ASP* 2.9 11.6 + - - +
55A ASP* 5.6 1.8 - - - +
57A ARG* 3.6 37.0 - - - +
63A VAL* 1.3 78.5 - - - +
65A LYS* 1.3 58.6 + - + +
67A VAL* 3.7 13.3 - - + +
68A ALA* 2.8 30.5 + - - +
175B LYS* 4.0 11.2 - - - +
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Residues in contact with LYS 65 (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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51A LEU* 3.8 30.8 - - + +
52A ARG 4.5 3.2 + - - -
53A ASP* 3.0 45.9 + - - +
54A ASN* 6.0 0.2 - - - +
55A ASP* 6.0 0.2 - - - -
64A LEU* 1.3 74.7 - - + +
66A ALA* 1.3 59.5 + - - +
68A ALA* 3.3 6.8 + - - +
69A ASN* 2.8 34.2 + - - +
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Residues in contact with ALA 66 (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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21A VAL* 3.7 12.6 - - + -
51A LEU* 3.8 17.3 - - + +
53A ASP* 4.8 0.2 + - - -
63A VAL* 3.3 10.3 + - + +
65A LYS* 1.3 77.2 - - - +
67A VAL* 1.3 57.2 + - - +
69A ASN* 3.1 9.3 + - - +
70A VAL* 3.0 31.0 + - - +
108A ASN* 3.6 36.1 - - - +
109A ALA* 3.6 9.4 - - + +
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Residues in contact with VAL 67 (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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9A ALA* 3.4 32.8 - - + +
10A TYR* 3.6 33.7 - - - +
11A GLU* 3.8 6.7 - - + +
21A VAL* 4.2 14.8 - - + -
63A VAL* 3.0 22.4 + - + +
64A LEU* 3.7 13.2 - - + +
66A ALA* 1.3 72.0 - - - +
68A ALA* 1.3 67.8 + - - +
70A VAL* 2.9 5.8 + - - +
71A ASN* 2.9 30.9 + - - +
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Residues in contact with ALA 68 (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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64A LEU 2.8 18.6 + - - +
65A LYS* 3.7 7.4 - - - +
67A VAL* 1.3 79.3 - - - +
69A ASN* 1.3 57.2 + - - +
71A ASN* 4.4 7.0 - - - +
72A GLU* 2.9 52.1 + - - +
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Residues in contact with ASN 69 (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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51A LEU* 3.4 21.0 - - - +
65A LYS* 2.8 15.2 + - - +
66A ALA 3.1 11.2 + - - +
68A ALA* 1.3 72.9 - - - +
70A VAL* 1.4 57.8 + - - +
73A THR* 3.3 16.3 + - - -
74A ILE* 2.8 31.5 + - - +
104A ASN* 3.5 12.3 + - - +
105A LEU* 2.9 42.7 + - + +
109A ALA* 4.2 3.4 - - + -
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Residues in contact with VAL 70 (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 VAL* 3.5 26.9 - - + +
8A ARG 3.8 8.7 - - - +
9A ALA* 3.6 29.2 - - + -
21A VAL* 4.7 4.3 - - + -
23A ALA* 4.9 0.9 - - + -
66A ALA 3.0 12.7 + - - +
67A VAL 2.9 6.5 + - - +
69A ASN* 1.4 75.6 - - - +
71A ASN* 1.3 60.5 + - - +
74A ILE* 4.1 6.1 - - + -
75A ALA* 3.0 31.0 + - - +
109A ALA* 3.8 30.7 - - + +
113A VAL* 3.6 12.3 - - + -
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Residues in contact with ASN 71 (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 VAL 4.1 4.1 - - - +
8A ARG* 3.1 13.2 - - - +
9A ALA 2.8 42.3 + - - -
67A VAL* 2.9 27.8 + - - +
68A ALA* 4.0 5.9 - - - +
70A VAL* 1.3 78.1 - - - +
72A GLU* 1.3 65.5 + - + +
75A ALA* 3.4 15.5 - - - +
76A ASP* 5.2 1.0 - - - +
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Residues in contact with GLU 72 (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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68A ALA* 2.9 29.4 + - - +
71A ASN* 1.3 85.2 - - + +
73A THR* 1.3 69.9 + - - +
74A ILE 3.5 0.4 - - - -
75A ALA 3.6 0.3 + - - -
76A ASP* 3.0 37.3 + - - +
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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