Contacts of the strand formed by residues 66 - 76 (chain G) in PDB entry 6CNB
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 SER 66 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1432A LYS* 3.4 26.0 - - - +
100F GLN* 5.4 1.8 - - - +
12G ARG* 3.4 4.9 - - - +
13G ILE* 2.9 63.2 + - - +
18G PHE* 3.7 19.1 - - - -
57G GLY* 5.4 0.9 - - - -
59G LEU* 4.9 3.1 - - - -
65G SER* 1.3 74.1 - - - +
67G TYR* 1.3 62.8 + - - +
68G ILE* 4.1 9.5 - - - +
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Residues in contact with TYR 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.7 9.8 - - + +
1147B PHE* 3.2 32.3 - + + -
10G LEU* 3.6 18.8 - - + -
11G VAL 3.4 2.5 - - - +
12G ARG* 3.0 51.6 + - + -
57G GLY* 3.1 3.0 - - - -
58G GLN 2.8 46.8 + - - +
59G LEU* 4.2 8.1 - - - +
60G LYS* 3.4 38.1 - - + -
63G ASP* 4.0 5.8 + - + -
65G SER 3.8 15.9 + - - -
66G SER* 1.3 77.6 + - - +
68G ILE* 1.3 59.1 + - - +
69G ASN 4.2 0.2 - - - -
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Residues in contact with ILE 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432A LYS* 5.9 1.8 - - + -
1434A THR* 3.6 22.9 - - + -
10G LEU* 4.6 1.1 - - - -
11G VAL* 2.9 36.3 + - - +
13G ILE* 4.1 24.2 - - + +
22G THR* 4.6 8.7 - - + -
26G ILE* 4.4 15.9 - - + +
54G VAL* 3.6 26.7 - - + -
55G GLU 3.6 11.7 - - - +
57G GLY* 3.5 16.8 - - - -
66G SER* 4.1 9.4 - - - +
67G TYR* 1.3 75.7 - - - +
69G ASN* 1.3 64.3 + - - +
70G VAL* 3.7 10.8 + - + +
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Residues in contact with ASN 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147B PHE* 5.8 1.8 - - - -
1148B GLN* 2.9 48.9 - - - +
9G ASP 3.4 7.0 - - - +
10G LEU* 3.7 30.4 - - + +
55G GLU* 2.7 40.7 + - - +
56G GLU 4.8 4.3 - - - +
57G GLY* 5.4 0.9 - - - -
58G GLN* 5.5 6.2 + - - +
67G TYR 4.2 0.8 + - - -
68G ILE* 1.3 75.2 - - - +
70G VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA* 3.3 5.6 - - - +
9G ASP 2.9 35.1 + - - +
11G VAL* 4.4 12.1 - - + -
26G ILE* 4.3 25.4 - - + -
30G LEU* 4.9 0.2 - - + -
51G LEU* 4.5 4.3 - - + -
52G LEU 4.6 1.6 - - - +
53G THR* 4.9 2.9 - - - -
54G VAL* 3.6 38.6 - - + -
55G GLU* 4.6 3.1 - - - -
68G ILE* 3.7 9.9 - - + +
69G ASN* 1.3 79.5 - - - +
71G THR* 1.3 65.6 + - - +
72G PHE* 4.2 18.8 - - + -
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Residues in contact with THR 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.6 6.7 - - + +
6G LYS* 3.8 15.3 - - + +
7G ILE 2.5 28.7 + - - -
8G ALA* 3.4 13.0 + - - +
51G LEU* 4.5 1.4 - - - +
52G LEU* 2.8 38.3 + - + +
53G THR* 3.4 26.0 - - + +
70G VAL* 1.3 78.2 - - - +
72G PHE* 1.3 69.4 + - - +
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Residues in contact with PHE 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LYS* 2.9 27.0 - - - +
7G ILE* 2.9 42.8 + - + -
9G ASP* 5.2 7.2 - - + -
30G LEU* 3.5 28.9 - - + -
34G PHE* 3.8 10.3 - + - -
48G ILE* 3.5 29.4 - - + -
50G ASP* 3.3 21.8 - - - +
51G LEU* 3.7 10.5 - - + -
52G LEU* 4.0 10.0 - - - +
70G VAL* 4.2 11.7 - - + -
71G THR* 1.3 83.7 + - - +
73G ARG* 1.3 75.7 + - - +
74G ALA* 3.5 13.7 - - + -
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Residues in contact with ARG 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1443A PRO* 3.2 28.1 - - - +
1444A LYS 5.0 2.2 + - - +
1445A ARG* 2.9 32.0 - - - +
8D ASN* 3.3 28.0 + - - +
9D ALA* 5.6 1.3 - - - +
4G LEU* 3.3 28.9 - - + +
5G SER 2.6 19.3 - - - +
6G LYS* 3.6 18.0 - - + +
49G TYR* 3.4 1.5 + - - -
50G ASP* 2.4 76.6 + - - +
52G LEU* 4.2 14.6 - - + +
72G PHE* 1.3 73.2 - - - +
74G ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 3.4 2.9 - - - -
5G SER* 2.9 22.8 + - - +
7G ILE* 5.0 6.4 - - + +
34G PHE* 5.2 0.4 - - + -
45G CYS* 3.8 13.2 - - - -
47G THR 3.3 14.4 - - - +
48G ILE* 3.7 11.7 - - + -
49G TYR 3.8 2.2 - - - +
72G PHE* 3.5 25.2 - - + -
73G ARG* 1.3 74.6 - - - +
75G VAL* 1.3 65.1 + - - +
76G VAL* 3.4 9.9 + - + +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.7 11.7 - - + -
16D VAL* 5.6 7.4 - - + -
20D LEU* 5.7 8.7 - - + -
2G PHE* 3.9 13.7 - - - +
3G ILE 3.4 12.3 - - - +
4G LEU* 3.7 19.7 - - + -
45G CYS* 3.1 3.3 - - - -
46G ILE* 2.4 57.9 + - + +
47G THR* 2.9 16.7 + - + +
49G TYR* 3.7 22.2 - - + -
74G ALA* 1.3 70.1 - - - +
76G VAL* 1.3 59.6 + - - +
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Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G PHE 2.4 28.7 + - - -
3G ILE* 2.8 41.9 + - + +
5G SER* 4.2 15.3 - - - +
39G ILE* 4.7 7.2 - - + -
42G VAL* 4.8 11.7 - - + -
43G GLY 3.8 13.9 - - - +
44G LEU 3.1 10.3 - - - +
45G CYS* 3.7 16.8 - - + +
46G ILE* 4.1 3.1 - - - -
74G ALA* 3.7 11.7 - - + +
75G VAL* 1.3 79.3 - - - +
77G PHE* 1.3 53.9 + - - +
78G LYS* 4.4 8.3 - - + -
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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