Contacts of the strand formed by residues 678 - 685 (chain A) in PDB entry 4BCX
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 VAL 678 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A PHE* 4.0 7.0 - - + -
674A GLU* 3.2 3.5 - - - -
675A ARG 2.9 38.0 + - - +
677A GLY* 1.3 79.6 - - - +
679A GLN* 1.3 67.3 + - - +
700A ALA* 5.5 2.7 - - + -
701A THR 3.3 10.5 - - - +
702A ASN* 4.1 5.6 - - - +
708A VAL* 3.4 34.8 - - + -
711A PHE* 5.1 10.8 - - + -
733A VAL* 6.1 1.8 - - + -
763A TYR* 4.0 23.8 - - + +
765A HIS* 3.8 19.3 - - + +
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Residues in contact with GLN 679 (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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671A LYS* 4.0 32.8 + - + +
673A PHE* 3.2 9.2 - - - +
674A GLU* 3.8 23.3 - - + +
677A GLY* 4.2 4.0 - - - +
678A VAL* 1.3 81.4 - - - +
680A LEU* 1.3 63.3 + - - +
681A ASN* 6.1 1.3 - - + -
699A THR 3.6 1.0 - - - +
700A ALA* 3.3 7.6 - - - +
701A THR* 2.9 40.3 + - - +
703A PHE* 3.4 30.9 - - + -
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Residues in contact with LEU 680 (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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671A LYS* 3.7 4.3 - - - +
672A VAL* 3.1 37.5 + - + +
673A PHE* 2.9 23.8 + - + +
679A GLN* 1.3 74.9 - - - +
681A ASN* 1.3 63.7 + - - +
698A ILE* 4.5 20.9 - - + -
699A THR 3.5 15.5 - - - +
700A ALA* 3.9 20.4 - - + -
711A PHE* 3.9 16.6 - - + -
713A CYS* 4.7 5.4 - - - -
759A LEU* 3.7 30.1 - - + -
761A LEU* 4.0 22.0 - - + -
774A PHE* 4.9 0.2 - - + -
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Residues in contact with ASN 681 (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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669A ASP* 3.0 37.3 + - - +
670A LEU 3.4 21.9 - - - +
671A LYS* 3.6 14.7 + - + +
679A GLN* 5.8 1.8 - - + -
680A LEU* 1.3 75.3 - - - +
682A LEU* 1.3 65.1 + - - +
683A SER* 3.9 5.5 + - - -
697A THR 3.4 1.7 - - - +
698A ILE* 3.3 5.5 - - - -
699A THR* 2.9 46.5 + - + +
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Residues in contact with LEU 682 (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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669A ASP* 3.2 10.4 - - - +
670A LEU* 2.9 35.2 + - + +
672A VAL* 3.6 33.9 - - + -
680A LEU* 5.1 0.9 - - + -
681A ASN* 1.3 76.7 - - - +
683A SER* 1.3 61.0 + - - +
684A PHE* 3.7 30.8 - - + -
696A ILE* 4.2 7.9 - - + -
697A THR 3.6 1.8 - - - -
698A ILE* 3.4 31.4 - - + -
757A LEU* 4.0 25.1 - - + -
759A LEU* 4.9 7.4 - - + -
776A VAL* 4.3 3.6 - - + -
779A LEU* 4.0 10.3 - - + -
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Residues in contact with SER 683 (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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669A ASP* 3.1 30.2 + - - -
681A ASN* 3.9 4.5 + - - -
682A LEU* 1.3 73.0 - - - +
684A PHE* 1.3 66.2 + - - +
685A ILE* 5.7 2.2 - - - -
695A LEU 3.6 0.8 - - - +
696A ILE* 3.3 9.4 - - - +
697A THR* 3.0 45.4 + - - +
699A THR* 5.0 4.2 + - - -
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Residues in contact with PHE 684 (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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667A ILE* 3.9 47.7 + - + +
668A PRO 3.6 24.9 - - - -
670A LEU* 4.1 11.0 - - + -
682A LEU* 3.7 32.3 - - + -
683A SER* 1.3 76.4 - - - +
685A ILE* 1.3 69.5 + - - +
694A LEU* 4.2 5.2 - - + -
695A LEU 3.6 2.9 - - - -
696A ILE* 3.9 30.1 - - + -
755A LEU* 5.3 0.2 - - + -
779A LEU* 3.9 28.7 - - + -
780A PRO* 4.0 12.6 - - + -
783A SER* 4.0 20.2 - - - -
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Residues in contact with ILE 685 (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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667A ILE* 5.0 0.7 - - - -
683A SER* 5.7 2.5 - - - -
684A PHE* 1.3 81.8 - - - +
686A ARG* 1.3 65.6 + - - +
687A PRO* 3.4 25.9 - - + +
694A LEU* 3.6 4.8 - - - +
695A LEU* 2.9 51.3 + - + +
697A THR* 6.0 1.8 - - - +
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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