Contacts of the strand formed by residues 64 - 77 (chain C) in PDB entry 3W1Y
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 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ARG* 3.2 51.4 - - + +
49C PHE 3.5 1.1 - - - -
50C THR* 2.8 39.9 + - - +
63C ASP* 1.3 88.9 + - - +
65C TYR* 1.3 60.9 + - - +
66C GLU* 4.1 2.7 + - + +
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Residues in contact with TYR 65 (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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48C ARG* 3.3 3.3 - - - -
49C PHE* 2.7 64.5 + + + +
51C VAL* 4.6 11.6 - - + +
64C GLN* 1.3 73.0 - - - +
66C GLU* 1.3 68.9 + - - +
67C ILE* 3.7 31.6 + - + +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 3.2 23.2 - - - +
47C GLU 3.3 13.0 - - - +
48C ARG* 3.0 39.1 + - - +
64C GLN* 4.1 3.6 + - + +
65C TYR* 1.3 88.0 - - - +
67C ILE* 1.3 71.1 + - - +
68C ARG* 3.9 33.2 + - + +
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Residues in contact with ILE 67 (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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13C PHE* 3.4 43.1 - - + -
45C ARG 3.5 1.7 - - - +
46C LYS* 3.9 0.7 - - - -
47C GLU* 2.9 45.2 + - + +
49C PHE* 3.7 32.3 - - + -
65C TYR* 3.7 26.9 - - + +
66C GLU* 1.3 78.9 - - - +
68C ARG* 1.3 61.9 + - - +
69C THR* 4.1 2.9 + - - +
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Residues in contact with ARG 68 (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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111B ASP* 3.0 35.4 + - - -
13C PHE* 3.3 32.7 - - - +
44C THR* 3.5 26.2 - - + +
45C ARG 3.0 9.2 - - - +
46C LYS* 4.5 14.7 - - - +
48C ARG* 5.8 0.4 - - - +
66C GLU* 3.9 33.9 + - + +
67C ILE* 1.3 76.3 - - - +
69C THR* 1.3 61.2 + - - +
70C HIS* 4.0 15.8 - - - +
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Residues in contact with THR 69 (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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11C LYS* 3.9 24.5 - - + -
12C ALA 3.6 10.1 - - - +
13C PHE* 3.6 19.1 - - + -
44C THR* 3.5 2.3 - - - -
45C ARG* 2.7 55.4 + - - +
47C GLU* 6.0 1.2 - - - +
67C ILE* 4.6 3.8 + - - +
68C ARG* 1.3 72.6 - - - +
70C HIS* 1.3 74.1 + - - +
71C LEU* 3.7 11.3 - - + +
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Residues in contact with HIS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 3.3 5.7 - - - -
12C ALA 2.9 29.9 + - - +
13C PHE 3.6 18.4 + - - -
15C HIS* 3.6 35.6 + + + +
18C ILE* 3.3 33.5 - - + +
44C THR* 3.2 33.1 + - + +
68C ARG* 4.3 20.6 - - + +
69C THR* 1.3 75.9 - - - +
71C LEU* 1.3 60.8 + - - +
72C ARG* 4.4 9.2 + - - +
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Residues in contact with LEU 71 (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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132A THR* 3.8 25.1 - - + -
9C ARG* 5.5 4.7 - - + +
10C LEU 3.4 6.3 - - - +
11C LYS* 3.7 33.4 - - + -
18C ILE* 3.9 0.2 - - - -
42C LEU* 3.1 42.7 + - + +
43C PRO 3.1 25.8 + - - +
45C ARG* 4.5 9.9 - - + +
69C THR* 3.7 16.6 - - + +
70C HIS* 1.3 84.8 - - - +
72C ARG* 1.3 86.5 + - - +
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Residues in contact with ARG 72 (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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9C ARG* 3.5 3.6 - - - +
10C LEU* 2.9 39.0 + - + +
15C HIS* 4.6 8.1 - - - +
18C ILE* 3.8 26.1 - - + +
19C ASP* 3.0 33.3 + - - -
22C THR* 3.5 35.9 - - + +
39C PRO* 4.9 5.4 - - + -
40C ILE 3.3 5.8 - - - +
41C PRO* 3.9 28.4 - - - +
42C LEU 4.1 6.1 + - - -
44C THR* 5.4 1.6 + - - -
70C HIS* 4.4 11.1 + - - +
71C LEU* 1.3 111.4 + - - +
73C LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 73 (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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95A PHE* 3.8 18.8 - - + -
130A GLU* 3.7 30.7 - - + +
7C ARG* 3.9 12.1 - - + +
8C ILE 3.3 4.3 - - - +
9C ARG* 3.6 37.2 - - + +
39C PRO* 3.5 5.4 - - - +
40C ILE* 2.8 52.2 + - + +
42C LEU* 3.7 37.5 - - + -
72C ARG* 1.3 75.3 - - - +
74C VAL* 1.3 63.8 + - - +
75C ASP* 5.4 1.1 - - - +
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Residues in contact with VAL 74 (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 ILE 3.9 0.7 - - - +
7C ARG* 3.7 0.2 - - - -
8C ILE* 2.8 43.5 + - + +
10C LEU* 4.4 10.3 - - + -
22C THR* 3.8 28.3 - - + -
25C ILE* 4.2 24.0 - - + -
26C VAL* 4.3 12.3 - - + +
36C VAL* 3.8 24.9 - - + -
37C ARG 3.8 4.0 - - - -
39C PRO* 4.5 3.1 - - + -
73C LEU* 1.3 79.2 - - - +
75C ASP* 1.3 68.5 + - - +
76C ILE* 4.2 7.9 - - + -
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Residues in contact with ASP 75 (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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38A THR* 4.0 0.9 - - - +
97A PHE* 5.3 2.4 - - - -
5C ARG* 3.0 20.6 + - - +
6C ILE 3.7 3.1 - - - +
7C ARG* 2.6 47.4 + - - +
36C VAL* 3.4 5.7 - - - +
37C ARG* 2.7 79.0 + - + +
40C ILE* 4.9 7.8 - - - +
73C LEU* 4.3 1.1 - - - +
74C VAL* 1.3 73.8 - - - +
76C ILE* 1.3 61.9 + - - +
77C VAL* 3.8 3.1 + - + +
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Residues in contact with ILE 76 (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 ARG* 3.5 6.4 - - - +
6C ILE* 2.8 48.2 + - + +
8C ILE* 3.5 26.7 - - + -
25C ILE* 4.5 2.5 - - + -
29C ALA* 3.9 22.2 - - + -
34C ALA* 3.6 27.8 - - + -
35C GLN 3.5 3.8 - - - +
36C VAL* 4.7 0.9 - - + -
74C VAL* 4.2 11.7 - - + -
75C ASP* 1.3 72.8 - - - +
77C VAL* 1.3 62.0 + - - +
79C PRO* 3.9 12.0 - - + +
83C THR* 4.0 13.0 - - + -
87C LEU* 3.8 25.1 - - + -
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Residues in contact with VAL 77 (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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100A ASN* 4.8 4.0 - - - +
5C ARG* 4.7 11.9 - - + +
34C ALA* 3.9 0.5 - - - +
35C GLN* 2.7 53.2 + - + +
37C ARG* 3.4 52.3 - - + +
75C ASP* 4.4 3.4 - - + +
76C ILE* 1.3 75.9 - - - +
78C GLU* 1.3 81.5 + - + +
79C PRO* 4.1 0.2 - - - -
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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