Contacts of the strand formed by residues 126 - 129 (chain B) in PDB entry 6VSB
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 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ILE* 6.4 0.7 - - + -
120B VAL 3.8 6.7 - - - +
121B ASN* 3.6 10.5 - - - +
125B ASN* 1.3 71.4 - - - +
127B VAL* 1.3 60.7 + - - +
128B ILE* 4.9 8.0 - - + +
170B TYR* 4.1 3.3 - - + +
171B VAL* 3.2 8.3 - - - +
172B SER* 3.0 41.4 + - - +
173B GLN 3.1 25.4 - - - +
174B PRO* 3.5 1.9 - - + +
175B PHE* 3.5 56.1 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 3.5 2.5 - - - +
120B VAL* 2.9 55.9 + - + +
122B ASN* 3.9 15.9 - - + +
125B ASN* 3.4 33.4 - - - +
126B VAL* 1.3 73.2 - - - +
128B ILE* 1.3 64.3 + - - +
129B LYS* 5.2 13.0 - - - -
170B TYR 3.9 3.1 - - - -
171B VAL* 4.0 6.5 - - + -
1319B NAG 4.5 15.9 - - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 4.4 8.5 - - + -
118B LEU 4.2 2.0 - - - -
119B ILE* 3.6 39.0 - - + -
126B VAL* 4.9 9.9 - - + -
127B VAL* 1.3 80.8 - - - +
129B LYS* 1.3 76.0 + - - +
168B PHE* 5.0 7.0 - - + -
169B GLU* 3.4 3.3 - - - +
170B TYR* 2.8 66.5 + - + +
175B PHE* 5.8 4.9 - - + -
203B ILE* 4.9 8.3 - - + -
227B VAL* 5.1 3.4 - - + -
229B LEU* 4.1 23.6 - - + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.1 26.6 - - - +
118B LEU* 3.3 14.9 + - + +
127B VAL* 5.2 12.6 - - + -
128B ILE* 1.3 84.6 - - - +
130B VAL* 1.3 61.5 + - - +
131B CYS* 3.5 15.0 - - - -
133B PHE* 3.5 35.6 - - + -
160B TYR* 5.2 7.7 - - - +
168B PHE* 3.4 9.2 - - - -
169B GLU* 4.1 11.2 - - + -
1319B NAG 4.9 12.4 + - - -
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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