Contacts of the strand formed by residues 982 - 986 (chain A) 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 ILE 982 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A SER* 3.1 8.5 - - - -
937A LEU* 2.7 52.7 + - + -
960A ILE* 4.2 22.4 - - + -
977A LEU* 4.5 16.2 - - + -
978A ALA 3.6 16.8 - - - +
979A THR* 3.2 13.7 + - - +
981A ASN* 1.3 86.0 - - + +
983A LEU* 1.3 59.4 + - - +
990A VAL* 3.7 21.8 - - + -
991A LYS 3.4 10.5 - - - +
992A ILE* 4.1 25.8 - - + -
1043A VAL* 5.2 4.0 - - + -
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Residues in contact with LEU 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A VAL* 4.1 2.2 - - + -
932A LEU* 3.7 27.4 - - + -
935A GLY 3.4 13.9 - - - +
936A SER* 4.0 7.4 - - - +
980A ARG 5.3 2.0 - - - +
981A ASN 4.9 0.9 - - - +
982A ILE* 1.3 76.8 - - - +
984A VAL* 1.3 63.8 + - - +
985A GLU 4.0 0.4 + - - -
990A VAL* 3.2 5.7 - - - +
991A LYS 2.7 34.4 + - - +
993A GLY* 3.6 23.8 - - - -
2001A IZA 3.5 76.3 - - + +
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Residues in contact with VAL 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A LEU* 3.8 9.1 - - - +
934A TYR* 3.3 41.8 + - + +
935A GLY 2.8 17.0 + - - +
937A LEU* 3.7 31.6 - - + -
940A TYR* 3.8 32.1 - - + -
956A TYR* 5.3 0.9 - - - +
983A LEU* 1.3 76.6 - - - +
985A GLU* 1.3 61.0 + - - +
986A ASN 3.1 27.6 - - - +
989A ARG 3.8 4.3 - - - +
990A VAL* 4.1 6.3 - - + -
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Residues in contact with GLU 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912A LYS* 5.3 4.3 + - - -
930A GLU* 4.6 4.9 - - - +
932A LEU* 3.8 26.5 - - + +
933A PRO* 4.0 11.8 - - + +
934A TYR* 3.3 16.3 - - - -
983A LEU 4.0 2.2 + - - -
984A VAL* 1.3 72.5 - - - +
986A ASN* 1.3 73.8 + - - +
989A ARG* 3.0 42.0 + - + +
990A VAL* 4.6 0.2 - - - +
991A LYS* 3.3 26.6 + - + +
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Residues in contact with ASN 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934A TYR* 3.9 15.9 - - + -
956A TYR* 4.7 0.9 + - - -
984A VAL* 3.1 19.7 - - - +
985A GLU* 1.3 94.2 + - - +
987A GLU* 1.3 63.4 + - - +
988A ASN* 2.8 36.5 + - - +
989A ARG* 3.1 27.7 + - - +
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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