Contacts of the strand formed by residues 6 - 11 (chain B) in PDB entry 5B2R
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 SER 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 1.3 77.2 + - - +
7B ILE* 1.3 66.2 + - - +
19B ALA 3.8 0.2 - - - +
20B VAL* 3.4 4.9 - - - -
21B ILE* 2.9 44.4 + - - +
22B THR 5.6 0.2 - - - -
756B PRO* 4.0 0.4 - - - -
757B GLU* 3.9 3.5 - - - +
758B ASN* 3.2 41.0 + - - -
760B VAL* 5.7 0.4 - - - -
991B ALA* 5.1 1.1 - - - -
995B THR* 3.7 19.6 - - - +
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Residues in contact with ILE 7 (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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5B TYR* 3.8 20.2 - - + +
6B SER* 1.3 76.8 - - - +
8B GLY* 1.3 71.0 + - - +
9B LEU* 3.8 25.1 - - + -
19B ALA 3.3 9.0 - - - +
20B VAL* 4.4 3.8 - - + -
744B VAL* 4.4 20.0 - - + -
747B LEU* 4.0 32.5 - - + -
748B VAL* 4.6 2.0 - - + -
756B PRO* 3.8 24.0 - - + -
758B ASN 3.0 6.3 + - - +
759B ILE* 3.3 12.1 - - + +
760B VAL* 2.9 27.4 + - - +
991B ALA* 4.1 3.4 - - - -
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Residues in contact with GLY 8 (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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7B ILE* 1.3 73.9 - - - +
9B LEU* 1.3 63.5 + - - +
18B TRP* 3.3 5.4 - - - -
19B ALA 2.9 31.4 + - - +
760B VAL 3.5 6.1 - - - -
987B ALA* 3.2 24.9 - - - -
991B ALA* 3.6 16.4 - - - +
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Residues in contact with LEU 9 (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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7B ILE* 3.8 14.6 - - + -
8B GLY* 1.3 81.3 - - - +
10B ALA* 1.3 60.4 + - - +
11B ILE* 4.1 5.2 - - + -
16B VAL* 4.4 3.6 - - + -
17B GLY 3.3 11.9 - - - +
18B TRP* 3.9 11.4 - - + -
740B THR* 3.6 31.2 - - + -
743B VAL* 4.3 8.7 - - + -
744B VAL* 3.6 20.0 - - + -
759B ILE* 3.6 25.8 - - + -
760B VAL 2.9 9.4 + - - +
761B ILE* 3.9 13.5 - - + -
762B GLU 3.1 23.0 + - - -
935B LEU* 4.1 1.8 - - + -
987B ALA* 3.9 2.3 + - - +
990B ASN* 3.2 10.1 + - - +
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Residues in contact with ALA 10 (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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9B LEU* 1.3 70.8 - - - +
11B ILE* 1.3 62.6 + - - +
15B SER* 3.7 2.8 + - - +
16B VAL* 3.3 6.2 - - - -
17B GLY 2.9 34.7 + - - +
762B GLU* 3.6 21.3 - - - +
983B HIS* 3.9 23.6 - - + +
986B ASP* 4.0 6.7 - - + +
987B ALA* 3.8 7.1 - - + +
990B ASN* 3.9 6.7 - - - +
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Residues in contact with ILE 11 (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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9B LEU* 4.6 6.5 - - + -
10B ALA* 1.3 73.3 - - - +
12B GLY* 1.3 61.7 + - - +
15B SER 4.1 1.6 - - - -
16B VAL* 4.8 1.8 - - + +
733B ILE* 4.4 8.9 - - + +
736B GLY* 4.1 18.8 - - - -
737B ILE* 4.4 2.7 - - + +
740B THR* 3.4 36.1 - - + +
761B ILE* 4.7 13.0 - - + -
762B GLU* 2.9 20.9 + - - +
763B MET* 3.5 27.1 - - + +
764B ALA* 3.0 26.2 + - - +
931B VAL* 3.8 30.3 - - + -
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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