Contacts of the strand formed by residues 24 - 29 (chain G) in PDB entry 3WUW
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 24 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ALA* 3.8 23.6 - - + -
13G TRP 3.5 11.4 - - - +
15G SER 3.3 26.0 - - - +
16G ALA* 4.7 0.2 - - - -
18G VAL* 4.1 13.0 - - + -
23G HIS* 1.3 78.7 - - - +
25G THR* 1.3 67.1 + - - +
60G ASN* 3.9 0.4 - - - -
61G MET* 2.9 52.5 + - + +
64G VAL* 4.0 16.4 - - + -
68G HIS* 5.8 0.2 - - + -
94G ILE* 4.3 12.8 - - + -
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G SER 3.5 1.4 - - - +
12G ALA* 3.3 3.6 - - - -
13G TRP* 2.8 43.8 + - - +
23G HIS* 5.5 1.7 + - - -
24G VAL* 1.3 74.6 - - - +
26G LEU* 1.3 63.7 - - - +
27G ARG* 3.9 8.5 + - + +
58G SER* 3.4 32.3 - - - -
59G PHE 3.2 11.0 - - - +
60G ASN* 3.0 25.8 + - + +
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Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 4.1 16.4 - - + -
11G SER 3.5 20.0 - - - +
12G ALA* 4.0 14.4 - - + -
25G THR* 1.3 72.9 - - - +
27G ARG* 1.3 60.8 + - - +
37G PHE* 4.1 5.2 - - + -
39G LEU* 4.0 19.7 - - + -
58G SER* 3.4 4.7 - - - -
59G PHE* 2.9 38.3 + - + +
61G MET* 3.6 25.3 - - + +
72G TYR* 3.9 37.5 - - + -
92G VAL* 4.2 13.5 - - + -
94G ILE* 4.2 5.4 - - + -
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Residues in contact with ARG 27 (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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15A PRO* 3.7 19.2 + - - +
16A GLY* 3.9 7.3 - - - -
90A ALA 5.9 0.8 + - - -
9G PHE 3.5 1.8 - - - +
10G LEU* 3.3 9.2 - - - +
11G SER* 2.9 43.1 + - - +
13G TRP* 5.3 13.8 - - + +
25G THR* 4.1 10.8 - - + +
26G LEU* 1.3 77.6 - - - +
28G CYS* 1.3 61.6 + - - +
29G HIS 3.9 0.7 - - - -
34G PHE* 3.5 54.4 - - + -
58G SER* 3.1 28.6 + - - +
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Residues in contact with CYS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PRO* 3.8 13.5 - - - -
9G PHE 3.7 2.7 - - - -
10G LEU* 4.5 0.7 - - + -
27G ARG* 1.3 74.8 - - - +
29G HIS* 1.3 60.8 + - - +
30G TYR* 3.7 3.1 + - - +
33G ARG 3.6 1.0 - - - +
34G PHE* 3.6 24.5 + - - -
35G ASN 5.1 1.4 - - - +
37G PHE* 3.4 45.4 - - + +
74G CYS* 2.0 48.7 - - + -
75G ARG 4.5 2.2 - - - -
76G GLY* 4.6 2.5 - - - -
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Residues in contact with HIS 29 (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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16A GLY 3.3 24.0 - - - +
17A ARG* 4.0 35.8 + - + +
8G PRO* 3.2 4.5 - - - +
9G PHE* 2.9 42.1 + - + +
27G ARG 3.9 0.8 - - - -
28G CYS* 1.3 69.8 - - - +
30G TYR* 1.3 62.2 + - - +
32G HIS* 3.6 39.7 + + + -
33G ARG 3.4 15.9 - - - -
34G PHE* 3.6 29.9 - + + -
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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