Contacts of the strand formed by residues 631 - 637 (chain A) in PDB entry 4HBN
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 LYS 631 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A GLU* 3.0 25.3 + - - -
630A LYS* 1.3 80.7 - - - +
632A MET* 1.3 59.9 + - - +
633A TYR* 3.2 29.5 + - + +
659A GLY 3.3 1.2 - - - +
663A LEU* 3.5 10.1 - - - +
669A ARG* 2.7 42.1 + - - +
683A SER* 3.5 23.0 + - - -
684A LEU 3.2 13.5 - - - +
685A SER* 4.0 7.0 - - - +
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Residues in contact with MET 632 (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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631A LYS* 1.3 71.1 - - - +
633A TYR* 1.3 71.5 + - - +
634A PHE* 3.4 34.5 - - + -
657A TYR* 3.4 37.5 - - + -
658A PHE 3.4 9.2 - - - +
659A GLY 3.2 20.2 - - - +
660A GLU* 3.9 15.9 - - + -
663A LEU* 3.5 19.1 - - + -
682A TYR 4.5 0.2 - - - -
683A SER* 3.2 7.1 - - - -
684A LEU* 2.6 49.2 + - + +
689A PHE* 4.3 11.4 - - - -
703A PHE* 3.8 9.0 - - + -
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Residues in contact with TYR 633 (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 GLU* 3.3 23.1 + - - -
616A PHE* 4.3 6.3 - + - -
622A ILE* 3.7 28.3 + - + +
623A ILE* 3.8 16.8 - - + -
631A LYS* 3.2 43.6 + - + +
632A MET* 1.3 82.3 - - - +
634A PHE* 1.3 63.7 + - - +
635A ILE 4.0 0.4 - - - -
657A TYR* 2.9 29.2 - - - +
658A PHE* 3.0 44.8 + + + -
669A ARG* 4.3 2.8 + - - -
681A LEU* 3.5 25.6 - - + -
682A TYR 3.3 4.3 - - - -
683A SER* 4.0 8.3 - - - -
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Residues in contact with PHE 634 (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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589A LEU* 4.5 10.8 - - + -
593A MET* 3.5 34.5 - - + -
595A LEU* 5.3 0.4 - - + -
596A PHE* 3.8 27.6 - + - -
607A MET* 4.5 3.8 - - - -
611A LEU* 3.8 26.7 - - + -
632A MET* 3.4 35.0 - - + -
633A TYR* 1.3 72.7 - - - +
635A ILE* 1.3 62.5 + - - +
636A GLN* 2.9 10.2 + - - +
656A SER 3.7 2.0 - - - -
657A TYR* 3.7 9.9 - + + -
681A LEU* 3.4 3.3 - - - -
682A TYR* 2.7 45.4 + - + +
684A LEU* 4.1 10.5 - - + -
703A PHE* 3.9 17.7 - + - -
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Residues in contact with ILE 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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589A LEU* 4.1 6.3 - - - +
633A TYR 4.0 0.2 - - - -
634A PHE* 1.3 70.5 - - - +
636A GLN* 1.3 61.8 + - - +
637A HIS 3.9 2.9 - - - +
638A GLY 3.3 33.9 - - - +
640A VAL* 3.6 31.9 - - + -
652A LEU* 3.6 22.7 - - + +
653A ALA 3.6 20.0 - - - +
654A ASP 3.7 1.8 - - - +
655A GLY 3.3 18.5 + - - -
656A SER* 2.8 20.4 + - - +
658A PHE* 3.7 23.3 - - + -
681A LEU* 3.6 15.7 - - + -
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Residues in contact with GLN 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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585A ASN 4.3 13.3 - - - +
586A CYS* 5.5 0.3 - - - -
588A LYS* 5.9 4.8 - - + +
589A LEU* 4.4 24.6 + - + +
613A PHE* 3.4 31.1 - - - -
634A PHE 2.9 7.1 + - - -
635A ILE* 1.3 74.7 - - - +
637A HIS* 1.3 66.7 + - + +
654A ASP* 3.3 21.5 - - - +
655A GLY 4.5 0.5 + - - -
680A ARG* 3.0 27.3 + - - +
682A TYR* 3.7 31.3 + - + -
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Residues in contact with HIS 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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635A ILE* 3.5 4.4 - - - +
636A GLN* 1.3 86.4 - - + +
638A GLY* 1.3 63.1 + - - +
654A ASP* 2.9 23.4 + - - +
678A TYR 3.8 7.3 - - - +
679A CYS* 3.3 2.3 - - - +
680A ARG* 2.6 81.5 + - + +
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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