Contacts of the strand formed by residues 634 - 639 (chain A) in PDB entry 4BLB
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 634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615A TRP* 5.2 1.3 - - + -
616A ASP 3.5 6.3 - - - +
617A ASP 4.5 3.0 - - - +
631A LEU* 4.1 13.0 - - + -
633A SER* 1.3 79.2 - - - +
635A HIS* 1.3 65.7 + - - +
636A LEU* 3.2 34.1 - - + -
689A TYR* 3.3 45.5 - - + -
696A LEU* 4.0 14.1 - - + -
698A ILE* 4.5 4.7 - - + -
728A GLU 3.7 4.9 + - - -
729A LYS* 3.5 14.4 - - + +
730A LYS* 3.2 21.0 + - - +
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Residues in contact with HIS 635 (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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615A TRP* 3.2 3.8 - - - -
616A ASP* 2.6 48.8 + - - +
617A ASP 4.0 13.3 - - - +
634A VAL* 1.3 76.1 - - - +
636A LEU* 1.3 70.2 + - - +
637A LYS* 4.2 21.7 - - + +
730A LYS* 3.4 40.9 - - + +
731A LEU 4.3 0.2 - - - -
732A LYS* 3.3 39.4 - - + +
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Residues in contact with LEU 636 (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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614A ALA 3.9 2.0 - - - +
615A TRP* 3.8 9.6 - - + -
634A VAL* 3.2 30.5 - - + -
635A HIS* 1.3 75.8 - - - +
637A LYS* 1.3 64.0 + - - +
638A PHE* 3.8 16.2 - - + -
671A ILE* 4.2 8.1 - - + -
673A PHE* 3.6 20.0 - - + -
696A LEU* 3.7 19.7 - - + -
698A ILE* 3.4 27.8 - - + -
708A MET* 6.1 1.8 - - + -
729A LYS* 4.7 9.6 - - + -
730A LYS 2.9 11.2 + - - +
731A LEU* 3.5 12.8 - - + +
732A LYS 2.9 26.3 + - - -
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Residues in contact with LYS 637 (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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613A CYS* 3.2 7.3 - - - +
614A ALA* 2.8 57.8 + - + +
615A TRP* 5.1 1.1 - - - +
616A ASP* 4.9 15.8 + - - +
635A HIS* 4.2 34.8 - - - +
636A LEU* 1.3 81.1 - - - +
638A PHE* 1.3 64.0 + - - +
732A LYS* 3.6 11.4 - - + +
734A SER* 5.2 8.3 - - - +
738A ASP* 4.9 7.0 - - - +
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Residues in contact with PHE 638 (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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612A LYS 4.0 3.4 - - - -
613A CYS* 3.8 11.2 - - + -
636A LEU* 3.8 14.1 - - + -
637A LYS* 1.3 77.1 - - - +
639A ASN* 1.3 64.1 + - - +
642A SER* 3.3 16.6 - - - +
643A GLY* 4.1 8.3 - - - +
646A ILE* 3.9 15.5 - - + -
662A TYR* 3.5 41.3 - + + -
671A ILE* 4.1 13.5 - - + -
673A PHE* 3.9 27.1 - + - -
731A LEU* 3.3 35.4 - - + -
732A LYS 3.0 8.2 + - - +
733A VAL* 3.3 6.1 - - + -
734A SER* 3.0 27.4 + - - -
738A ASP* 4.8 5.2 - - - -
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Residues in contact with ASN 639 (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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611A ALA* 4.9 1.3 - - - +
612A LYS* 3.3 36.6 + - + +
638A PHE* 1.3 75.3 - - - +
640A GLN* 1.3 53.7 + - - +
641A GLU* 3.8 18.8 + - - +
642A SER* 2.5 43.7 + - - -
643A GLY* 2.7 31.9 + - - -
733A VAL* 3.9 4.1 - - - +
734A SER 4.0 8.7 - - - +
736A LEU* 3.8 28.8 - - + +
738A ASP* 4.6 4.9 + - - +
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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