Contacts of the strand formed by residues 121 - 126 (chain B) in PDB entry 2B7O
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.1 18.6 - - + +
82B LEU* 3.7 29.4 - - + +
110B ALA* 4.0 22.0 - - + +
113B LEU* 3.8 12.8 - - + +
114B THR* 3.2 45.6 + - - +
117B ALA* 5.2 0.2 - - + -
119B MSE 4.1 1.1 - - - +
120B PRO* 1.3 79.1 - - - +
122B VAL* 1.3 66.2 + - - +
123B LYS* 3.7 17.7 + - + -
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Residues in contact with VAL 122 (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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67B LEU* 3.8 28.7 - - + -
70B GLN* 3.8 40.4 - - + +
71B LEU* 4.0 10.1 - - + -
74B VAL* 4.0 11.4 - - + -
79B ALA* 4.8 6.1 - - + -
80B PHE 2.7 13.1 + - - +
81B LEU* 3.7 6.8 - - + +
82B LEU* 2.8 29.1 + - - +
120B PRO* 5.6 1.8 - - + -
121B VAL* 1.3 73.9 - - - +
123B LYS* 1.3 61.5 + - - +
124B VAL* 4.1 9.4 - - + -
244B TYR* 4.3 9.9 - - + -
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Residues in contact with LYS 123 (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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82B LEU* 3.6 6.1 - - + -
106B LEU* 3.9 20.6 - - + +
107B LEU* 3.9 29.4 - - + -
110B ALA* 3.5 33.3 - - + +
121B VAL* 3.7 19.2 + - + +
122B VAL* 1.3 75.8 - - - +
124B VAL* 1.3 60.3 - - - +
125B ALA 4.1 0.4 - - - -
241B ALA* 4.7 5.2 - - - +
242B GLU* 3.4 33.4 + - - +
243B ILE* 3.5 5.8 - - + -
244B TYR* 2.9 31.1 + - - -
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Residues in contact with VAL 124 (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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67B LEU* 4.5 7.4 - - + -
71B LEU* 5.3 1.1 - - + -
81B LEU* 3.6 23.6 - - + -
82B LEU 2.9 12.1 + - - +
83B GLN* 3.1 20.9 - - + +
84B GLY 3.0 24.1 + - - -
106B LEU* 4.3 4.3 - - - +
122B VAL* 4.1 10.3 - - + -
123B LYS* 1.3 77.7 - - - +
125B ALA* 1.3 61.5 + - - +
244B TYR* 3.6 17.5 - - + +
246B SER* 3.3 33.7 - - - +
278B THR* 3.8 13.5 - - + -
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Residues in contact with ALA 125 (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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84B GLY 3.2 9.2 - - - +
85B GLY* 5.7 0.4 - - - -
102B ASN* 6.5 0.4 - - + -
103B VAL* 6.3 1.3 - - + -
106B LEU* 4.3 7.2 - - + -
123B LYS 4.1 1.0 - - - -
124B VAL* 1.3 73.8 - - - +
126B ARG* 1.3 55.9 + - - +
127B ILE* 3.4 31.3 + - + -
243B ILE* 3.7 18.0 - - + +
244B TYR 2.8 11.4 + - - +
245B ALA* 3.8 0.3 - - - -
246B SER* 2.8 34.8 + - - -
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Residues in contact with ARG 126 (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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83B GLN* 4.7 0.4 - - + -
84B GLY* 2.9 18.5 + - - +
85B GLY* 3.8 8.6 - - - +
86B ASP* 2.8 38.6 + - - +
87B CYS* 2.9 28.5 + - - +
89B GLU* 4.3 6.6 - - - +
102B ASN* 5.8 0.7 + - - -
125B ALA* 1.3 67.6 - - - +
127B ILE* 1.3 64.4 + - - +
130B GLN* 3.4 19.7 - - + +
246B SER* 3.5 11.9 - - - +
280B TRP* 3.3 17.0 - - + -
409B HIS* 3.0 40.0 - - + -
410B VAL 3.6 17.7 - - - -
411B GLU* 3.7 15.5 + - - +
701B MN 4.2 0.8 + - - -
703B PEP 3.1 36.4 + - - -
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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