Contacts of the strand formed by residues 874 - 877 (chain B) in PDB entry 6AHU
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 MET 874 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B GLY* 4.4 2.2 - - - -
700B THR* 2.9 39.0 - - - +
701B LEU 5.4 1.3 - - - +
702B ALA* 5.2 7.4 - - + -
872B HIS 4.6 5.8 - - - +
873B THR* 1.3 77.8 - - - +
875B ILE* 1.3 64.3 + - - +
876B CYS* 3.9 9.8 + - - -
963B LEU* 3.7 17.9 - - + -
965B GLY 3.4 5.6 - - - +
966B PHE* 3.7 25.1 - - + -
1007B LEU* 3.5 3.1 - - - +
1008B ARG* 2.8 75.0 + - - +
1010B PRO* 5.0 13.5 - - + -
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Residues in contact with ILE 875 (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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861B LEU* 3.8 26.5 - - + -
874B MET* 1.3 74.5 - - - +
876B CYS* 1.3 56.5 + - - +
963B LEU* 3.3 4.3 - - - +
964B LEU* 2.8 45.1 + - + -
965B GLY* 2.5 34.2 + - - +
966B PHE 4.0 9.4 - - - +
967B VAL* 3.8 18.8 - - + -
985B VAL* 5.0 7.6 - - + -
1005B VAL* 3.8 19.3 - - + +
1006B LEU 3.8 4.3 - - - +
1007B LEU* 3.7 20.9 - - + -
1020B ILE* 5.0 9.0 - - + -
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Residues in contact with CYS 876 (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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874B MET* 3.9 6.0 + - - -
875B ILE* 1.3 77.9 - - - +
877B VAL* 1.3 64.3 + - - +
878B PRO* 3.5 1.7 - - - +
961B ARG* 3.9 16.6 - - + -
962B THR 3.3 4.5 - - - +
963B LEU* 3.9 18.6 - - - -
964B LEU* 3.9 3.6 - - - -
1005B VAL* 3.3 9.4 - - - +
1006B LEU* 2.9 26.6 + - + +
1008B ARG* 4.2 24.0 - - - -
1015B TYR* 3.7 34.1 - - + -
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Residues in contact with VAL 877 (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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715B TRP* 4.8 5.4 - - + -
876B CYS* 1.3 69.6 - - - +
878B PRO* 1.3 78.9 - - - +
961B ARG* 3.4 21.9 - - - +
962B THR* 2.5 39.5 + - + +
964B LEU* 3.7 31.4 - - + -
989B GLY 5.0 4.0 - - - +
993B MET* 3.7 25.6 - - + -
1005B VAL* 4.7 1.1 - - + -
1006B LEU* 5.6 0.2 - - - -
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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