Contacts of the strand formed by residues 10 - 15 (chain G) in PDB entry 3B4V
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 GLY 10 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G GLY* 1.3 69.2 - - - +
11G VAL* 1.3 63.4 + - - -
29G ASP 3.1 10.7 + - - -
30G VAL 2.8 36.8 + - - -
45G TRP* 3.7 14.5 - - - -
46G SER 3.6 12.6 - - - -
47G ASN 4.5 6.5 - - - -
49G THR* 4.1 9.0 - - - -
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Residues in contact with VAL 11 (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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10G GLY* 1.3 78.8 - - - +
12G CYS* 1.3 62.6 + - - +
13G TRP* 3.4 36.6 - - + +
25G VAL* 4.2 14.4 - - + -
27G GLN 3.4 11.2 - - - +
28G THR* 4.3 11.9 - - + -
29G ASP 4.9 0.9 - - - +
45G TRP* 3.4 6.5 - - - +
46G SER 3.0 33.4 + - - +
48G LEU 3.9 11.9 - - - +
49G THR* 4.1 12.6 - - + +
55G ILE* 3.9 28.7 - - + -
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Residues in contact with CYS 12 (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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11G VAL* 1.3 73.5 - - - +
13G TRP* 1.3 55.7 + - - +
25G VAL* 3.9 1.9 - - - -
26G LEU* 2.8 41.5 + - - +
27G GLN* 2.7 22.5 + - + +
30G VAL* 3.7 14.5 - - + +
35G CYS* 2.0 52.9 - - + -
43G THR* 3.5 16.8 - - - -
44G ALA 3.4 2.9 - - - -
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Residues in contact with TRP 13 (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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11G VAL* 3.4 29.0 - - + +
12G CYS* 1.3 74.8 - - - +
14G LEU* 1.3 61.6 + - - +
22G CYS* 3.6 46.2 - - + -
23G SER 3.9 7.6 - - - -
24G LEU 3.5 23.1 - - - -
25G VAL* 3.5 18.8 - - + -
26G LEU* 4.2 5.8 - - - +
43G THR* 3.5 9.4 + - - -
44G ALA 2.7 35.3 + - - +
46G SER* 3.4 25.9 - - - -
55G ILE* 3.5 46.0 - - + +
56G ASN 5.5 0.4 - - - -
58G LEU* 4.9 0.7 - - + -
59G GLY* 3.8 9.6 - - - -
64G VAL* 3.5 26.4 - - + +
66G CYS* 4.1 6.5 - - - -
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Residues in contact with LEU 14 (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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1F GLY 4.2 13.9 - - - +
2F LEU* 4.8 11.4 - - + -
13G TRP* 1.3 75.7 - - - +
15G GLN* 1.3 69.0 + - - +
16G GLN* 3.6 29.6 + - - +
22G CYS* 3.9 1.6 - - - -
23G SER* 3.8 19.2 + - - -
24G LEU* 2.8 31.6 + - + +
26G LEU* 3.6 30.3 - - + -
40G ASN* 4.2 16.4 - - - +
42G ASP* 3.5 25.4 - - - +
43G THR* 4.9 0.4 - - - -
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Residues in contact with GLN 15 (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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14G LEU* 1.3 76.1 - - - +
16G GLN* 1.3 62.1 + - - +
17G GLY 4.9 0.7 - - - -
20G ALA* 3.4 38.7 - - + +
21G THR 4.0 4.9 - - - -
22G CYS* 3.8 20.4 - - - -
41G ILE 5.0 0.8 + - - -
42G ASP* 2.9 54.3 + - + +
44G ALA* 3.8 12.6 - - + +
66G CYS* 4.7 3.8 - - - +
68G PRO* 3.9 35.1 - - - +
92G ARG* 4.8 9.4 + - - +
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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