Contacts of the strand formed by residues 913 - 917 (chain B) in PDB entry 2B7A
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 TYR 913 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B THR* 3.5 22.6 + - - +
899B ILE* 3.7 23.2 - - + +
902B LEU* 3.9 30.3 + - + +
903B LYS* 3.7 50.4 + - + +
905B LEU 5.5 3.1 + - - +
911B VAL 3.6 3.4 + - - -
912B LYS* 1.3 76.3 - - - +
914B LYS* 1.3 61.8 + - - +
915B GLY* 3.4 34.5 - - - -
916B VAL* 3.8 12.5 + - - +
927B LEU* 3.6 17.9 - - + -
928B ILE 4.1 1.8 - - - -
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Residues in contact with LYS 914 (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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841B PRO 4.3 1.2 - - - +
842B THR* 3.1 21.1 + - - -
844B PHE* 3.6 13.4 - - + -
877B GLU* 3.4 32.3 + - - +
878B VAL 5.4 0.9 - - - -
879B VAL* 3.7 24.5 - - + -
912B LYS* 3.7 6.1 + - + +
913B TYR* 1.3 79.9 - - - +
915B GLY* 1.3 58.6 + - - +
928B ILE* 2.8 24.1 + - + +
929B MET 3.9 4.9 - - - +
930B GLU* 3.8 31.6 - - + +
931B TYR 5.3 0.4 - - - +
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Residues in contact with GLY 915 (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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842B THR* 3.1 20.2 - - - -
844B PHE* 3.9 4.3 - - - -
913B TYR* 3.4 22.8 - - - -
914B LYS* 1.3 79.5 - - - +
916B VAL* 1.3 59.7 + - - +
927B LEU* 3.8 0.5 - - - +
928B ILE* 2.8 35.2 + - - +
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Residues in contact with VAL 916 (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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842B THR 2.9 7.3 + - - +
843B GLN* 3.5 29.9 - - - +
844B PHE* 2.9 26.2 + - - +
899B ILE* 3.6 44.0 - - + -
913B TYR* 3.8 6.5 - - - +
915B GLY* 1.3 78.6 - - - +
917B CYS* 1.3 60.0 + - - +
918B TYR* 3.6 21.1 - - + +
925B LEU* 4.1 10.3 - - + -
926B LYS 3.3 6.7 - - - +
928B ILE* 3.9 4.9 - - - +
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Residues in contact with CYS 917 (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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844B PHE* 3.4 21.3 - - + +
845B GLU 4.4 0.4 - - - -
846B GLU* 3.8 32.5 - - - -
849B LEU* 4.4 4.9 - - + -
916B VAL* 1.3 74.0 - - - +
918B TYR* 1.3 66.2 + - - +
924B ASN 3.5 3.5 - - - +
925B LEU* 3.4 7.5 - - - +
926B LYS* 2.9 65.4 + - + -
928B ILE* 4.1 13.5 - - + -
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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