Contacts of the strand formed by residues 101 - 106 (chain W) in PDB entry 1VPP
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 LYS 101 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28W PRO* 4.3 4.3 - - - -
57W CYS* 3.8 0.9 - - - -
70W PRO* 3.5 5.2 - - - +
71W THR* 2.8 36.0 + - - +
72W GLU* 3.1 40.4 + - + +
99W HIS 3.5 0.8 - - - -
100W ASN* 1.3 87.8 + - + +
102W CYS* 1.3 64.8 + - - +
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Residues in contact with CYS 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W CYS* 3.5 25.1 - - - +
27W HIS* 3.6 7.0 - - - -
28W PRO* 3.5 28.1 - - - +
57W CYS* 2.0 51.4 - - - -
69W VAL 3.1 7.6 - - - +
71W THR* 4.0 2.7 - - - -
101W LYS* 1.3 77.4 - - - +
103W GLU* 1.3 64.3 + - - +
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Residues in contact with GLU 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W TYR* 6.3 0.9 - - - -
26W CYS* 3.7 9.6 - - - -
69W VAL* 2.9 32.3 + - + +
71W THR* 3.4 20.4 - - + +
102W CYS* 1.3 74.6 - - - +
104W CYS* 1.3 66.3 + - - +
105W ARG* 2.6 45.7 + - + +
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Residues in contact with CYS 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W TYR* 3.3 27.6 + - - +
26W CYS* 3.6 18.2 - - - -
61W CYS* 2.1 52.5 - - + -
66W LEU* 4.3 15.6 - - + +
67W GLU 3.3 5.6 - - - -
103W GLU* 1.3 75.6 - - - +
105W ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66W LEU* 3.3 6.2 - - - -
67W GLU* 2.9 30.4 + - + +
69W VAL* 3.8 26.6 - - + +
70W PRO 4.9 4.0 + - - -
71W THR* 3.6 21.6 - - - +
103W GLU* 2.6 31.3 + - + +
104W CYS* 1.3 75.8 - - - +
106W PRO* 1.3 80.8 - - + +
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Residues in contact with PRO 106 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65W GLY 3.2 11.9 - - - +
66W LEU* 3.6 12.8 - - + -
67W GLU* 4.4 4.3 - - - +
105W ARG* 1.3 94.4 - - + +
107W LYS* 1.3 68.0 + - - +
108W LYS* 4.9 0.7 - - - +
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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