Contacts of the strand formed by residues 872 - 875 (chain A) in PDB entry 3I7P
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 872 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A LYS* 5.9 1.8 - - - +
815A SER* 3.6 10.1 - - - -
870A VAL* 3.2 2.8 - - - +
871A TYR* 1.3 82.3 - - - +
873A MET* 1.3 64.5 + - - +
882A ALA* 3.5 1.2 - - - -
883A SER* 2.8 36.1 + - - +
912A LEU 3.8 12.6 - - - -
913A TYR* 3.7 5.1 - - - -
914A LEU* 3.3 31.8 + - - +
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Residues in contact with MET 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A SER* 3.9 10.7 - - - +
816A LEU 5.1 0.3 - - - +
817A VAL* 3.0 35.8 - - + +
830A ILE* 3.6 30.3 - - - +
832A GLY* 3.7 20.9 - - - -
848A ILE* 4.0 11.9 - - + -
870A VAL* 2.7 40.6 - - + -
872A SER* 1.3 73.4 - - - +
874A VAL* 1.3 60.5 + - - +
880A LEU* 4.2 8.3 - - + -
881A LEU 3.2 16.8 - - - +
882A ALA* 3.6 13.7 - - + +
914A LEU* 4.2 3.4 - - - -
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A VAL* 4.6 2.2 - - - -
873A MET* 1.3 74.6 - - - +
875A GLU* 1.3 85.6 + - + +
876A PHE 3.5 0.2 + - - -
880A LEU* 3.6 9.9 - - - +
881A LEU* 2.9 48.4 + - + +
914A LEU* 4.4 12.1 - - + +
915A LYS* 4.6 12.8 - - - +
916A THR* 3.2 35.0 - - + +
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Residues in contact with GLU 875 (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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817A VAL* 5.0 5.9 - - + +
819A CYS* 3.7 37.7 - - + -
820A LYS 4.3 8.1 - - - +
821A LEU* 4.7 0.2 - - + -
874A VAL* 1.3 91.2 - - + +
876A PHE* 1.3 79.6 + - - +
877A ASN* 3.4 1.0 - - - -
878A GLY 3.2 18.7 + - - +
879A LYS 3.8 8.3 - - - +
880A LEU* 4.6 2.9 - - + -
916A THR* 4.3 4.5 - - - +
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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