Contacts of the strand formed by residues 105 - 109 (chain B) in PDB entry 3VZC
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 LEU 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.4 26.0 - - + +
77B VAL* 5.6 0.4 - - + -
84B MET* 4.2 17.9 - - + -
87B VAL* 4.5 5.4 - - + -
88B VAL* 3.6 30.7 - - + -
91B LEU* 4.1 22.9 - - + -
101B ILE* 5.0 0.7 - - + -
103B LYS 3.2 22.4 - - - +
104B PRO* 1.3 78.8 - - - +
106B CYS* 1.3 60.7 + - - +
359B PHE* 3.8 23.1 - - + -
360B TRP 2.8 11.1 + - - +
361B MET* 3.2 11.8 - - + -
362B VAL* 3.1 25.1 + - - +
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Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 5.8 1.6 - - + -
75B LEU 2.9 7.1 + - - +
76B VAL* 3.9 18.2 - - + -
77B VAL 2.9 26.2 + - - -
84B MET* 3.5 8.9 - - - +
105B LEU* 1.3 77.0 - - - +
107B SER* 1.3 65.7 + - - +
108B LEU* 3.9 24.2 - - - -
138B CYS 5.1 0.7 - - - -
142B LEU* 3.9 18.8 - - + -
361B MET* 4.6 3.6 - - - -
362B VAL* 3.7 35.0 - - + +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.7 5.4 + - - +
79B SER 5.6 1.7 + - - -
80B GLY 5.4 4.9 + - - -
81B ASP* 5.3 1.9 + - - -
84B MET* 3.8 19.7 - - - +
106B CYS* 1.3 78.0 - - - +
108B LEU* 1.3 70.0 + - - +
109B PRO* 4.0 2.4 - - - +
116B LEU* 4.4 19.0 - - - +
117B ALA* 4.1 18.9 + - - +
120B LEU* 4.6 15.2 - - - +
138B CYS* 3.8 14.2 - - - +
361B MET* 4.6 2.9 - - - -
362B VAL 5.9 0.2 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 5.4 0.4 - - + -
38B VAL* 3.9 33.7 - - + -
76B VAL* 3.7 23.1 - - + -
77B VAL 2.8 12.4 + - - +
78B MET* 3.1 34.2 - - + +
79B SER 3.3 5.4 + - - +
106B CYS* 3.9 15.5 - - - -
107B SER* 1.3 82.9 + - - +
109B PRO* 1.3 69.5 - - + +
135B LEU* 3.9 10.1 - - + +
138B CYS* 3.6 11.4 - - + +
139B THR* 3.6 32.3 - - - +
142B LEU* 4.6 8.1 - - + -
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.6 1.0 - - - +
78B MET* 4.5 0.3 - - - +
79B SER 3.8 1.8 - - - +
107B SER* 4.1 0.8 - - - +
108B LEU* 1.3 87.0 - - + +
110B ALA* 1.3 61.1 + - - +
114B ASN* 3.4 33.2 - - + +
117B ALA* 3.9 17.2 - - + -
131B ASN* 5.0 2.0 - - - +
134B LEU* 3.9 19.3 - - + -
135B LEU* 3.3 47.5 - - + +
138B CYS* 3.9 14.8 - - + -
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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