Contacts of the strand formed by residues 100 - 106 (chain G) in PDB entry 2VTX
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 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G PHE 4.2 0.2 - - - +
31G GLU* 3.5 2.2 - - - +
32G PHE* 2.9 58.7 + - + +
45G LEU* 4.0 15.0 - - + -
65G ILE* 4.4 8.7 - - + -
67G ASP* 4.1 14.4 - - - +
96G LEU* 3.8 39.7 - - + -
97G ASP 4.4 6.5 - - - +
98G PRO* 4.4 3.8 - - + -
99G PRO* 1.4 77.1 - - - +
101G THR* 1.3 66.1 + - - +
102G PHE* 4.5 8.5 - - + -
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Residues in contact with THR 101 (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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29G THR* 3.1 32.5 - - + -
30G PHE 3.5 10.3 - - - +
31G GLU* 3.6 22.5 + - + +
65G ILE* 3.4 9.0 - - - +
66G VAL* 2.8 54.7 + - + +
67G ASP* 5.2 0.2 + - - -
100G VAL* 1.3 78.5 + - - +
102G PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 102 (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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19G TRP* 3.7 26.0 - + - -
21G CYS* 4.5 3.1 - - - -
23G LEU* 4.3 9.4 - - + +
28G LYS 3.6 1.3 - - - +
29G THR* 3.2 5.5 - - - +
30G PHE* 2.9 43.0 + + - +
32G PHE* 4.5 8.1 - - + -
45G LEU* 3.8 15.0 - - + -
47G LEU* 3.8 37.9 - - + -
63G VAL* 4.4 8.3 - - + -
64G GLU 3.3 5.2 - - - +
65G ILE* 4.1 22.7 - - + -
78G ILE* 4.6 1.1 - - + -
96G LEU* 4.3 6.5 - - + -
100G VAL* 4.5 9.0 - - + -
101G THR* 1.3 79.2 - - - +
103G ARG* 1.3 61.3 + - - +
113G ILE* 3.6 31.2 - - + -
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Residues in contact with ARG 103 (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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23G LEU* 4.2 4.3 - - - -
28G LYS* 3.3 11.0 - - + +
29G THR* 3.5 28.6 - - + +
63G VAL* 3.3 1.4 - - - -
64G GLU* 2.6 59.4 + - + +
66G VAL* 3.4 30.8 - - + +
73G GLU 5.9 1.4 - - - +
75G SER* 3.0 27.7 + - - -
102G PHE* 1.3 75.8 - - - +
104G LEU* 1.3 68.6 + - - +
105G LYS* 3.3 4.8 + - - +
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Residues in contact with LEU 104 (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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23G LEU* 4.0 9.8 - - + +
24G ASN* 3.7 38.6 - - - +
28G LYS* 2.9 41.7 + - + +
61G HIS* 4.5 3.8 - - + -
62G ILE 3.3 9.6 - - - +
63G VAL* 4.4 0.4 - - - +
103G ARG* 1.3 73.6 - - - +
105G LYS* 1.3 64.1 + - - +
106G ALA* 3.3 20.2 + - - +
107G GLY 3.4 18.8 - - - +
108G SER 4.2 5.4 - - - -
109G GLY* 4.3 1.6 - - - +
111G LEU* 4.0 37.2 - - + -
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Residues in contact with LYS 105 (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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28G LYS* 4.9 8.3 + - - +
62G ILE* 2.9 38.4 + - + +
64G GLU* 3.4 40.4 - - + +
77G PRO* 4.0 11.4 - - + -
103G ARG* 3.3 5.6 + - - +
104G LEU* 1.3 72.2 - - - +
106G ALA* 1.3 60.1 + - + +
112K TYR* 3.8 24.5 + - - -
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Residues in contact with ALA 106 (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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28G LYS* 6.1 0.7 - - - +
60G PHE 3.7 9.9 - - - +
61G HIS* 3.4 2.6 - - - -
62G ILE* 3.3 30.5 + - + +
104G LEU* 3.3 13.3 - - - +
105G LYS* 1.3 79.8 - - + +
107G GLY* 1.3 67.2 + - - +
54K ASP* 3.5 30.7 - - - +
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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