Contacts of the strand formed by residues 682 - 695 (chain A) in PDB entry 5C58
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 682 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A ARG* 5.4 7.3 - - - +
650A LYS* 4.0 41.1 + - + +
651A VAL 3.9 3.3 - - - +
652A ASP* 2.8 45.0 + - + +
679A ASN* 3.8 5.0 + - - -
681A SER* 1.3 79.3 - - - +
683A THR* 1.3 64.1 + - - +
684A ARG* 4.2 2.0 - - + -
712A ASN* 4.0 8.1 - - - +
713A GLU* 3.9 9.4 + - - +
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Residues in contact with THR 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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649A THR 3.7 1.2 - - - +
650A LYS* 3.6 2.4 - - - -
651A VAL* 2.8 46.3 + - - +
654A TYR* 3.3 32.9 - - + +
679A ASN* 3.3 21.8 + - - +
681A SER 4.6 0.2 + - - -
682A LYS* 1.3 73.4 + - - +
684A ARG* 1.3 62.4 + - - +
685A PHE* 3.9 25.9 + - + -
712A ASN* 3.6 23.8 - - - +
713A GLU 5.9 0.2 - - - +
760A ALA* 5.4 3.1 - - + +
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Residues in contact with ARG 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 5.5 0.2 + - - -
648A ASP* 3.2 38.2 + - - +
649A THR 3.4 3.6 - - - +
650A LYS* 4.2 32.4 - - + +
682A LYS* 4.2 2.0 - - + -
683A THR* 1.3 74.5 - - - +
685A PHE* 1.3 63.3 + - - +
686A ARG* 3.2 49.8 - - + +
709A ILE 5.2 1.2 - - - +
710A GLY* 5.7 1.5 - - - -
711A LYS 6.1 0.7 - - - +
712A ASN* 2.8 34.3 + - + +
762A LEU* 3.9 11.4 - - - +
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Residues in contact with PHE 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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165A ARG* 3.1 28.5 - - + +
166A GLY* 3.7 21.1 - - - -
167A ILE* 3.6 33.4 - - + -
647A PHE* 3.7 9.3 - - + -
648A ASP* 3.6 0.5 - - - -
649A THR* 2.6 54.0 + - - +
651A VAL* 4.3 10.3 - - + -
654A TYR* 3.9 26.2 - + - -
683A THR* 3.9 28.7 - - + -
684A ARG* 1.3 76.0 - - - +
686A ARG* 1.3 58.9 + - - +
760A ALA* 4.9 10.1 - - - -
761A TYR 5.9 0.2 - - - -
762A LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 3.7 21.7 + - - +
647A PHE* 3.2 25.0 - - - +
648A ASP* 3.5 11.7 - - + +
684A ARG* 3.2 44.3 + - + +
685A PHE* 1.3 74.8 - - - +
687A GLY* 1.3 58.8 + - - +
708A MET* 3.9 6.6 - - - +
709A ILE* 3.1 59.6 + - + +
710A GLY* 4.7 8.7 - - - -
762A LEU* 4.2 4.6 - - - +
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 3.3 10.9 - - - -
647A PHE* 3.1 44.4 + - - -
686A ARG* 1.3 78.3 - - - +
688A LEU* 1.3 62.0 + - - -
707A HIS 3.1 13.7 - - - -
709A ILE* 4.2 10.8 - - - -
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL* 5.0 7.0 - - + -
645A ALA 3.3 7.2 - - - +
646A TYR* 3.6 35.0 - - + +
647A PHE* 4.6 1.2 - - - -
687A GLY* 1.3 74.7 - - - -
689A GLU* 1.3 67.8 + - - +
690A TYR* 3.3 35.9 - - + +
705A TYR 4.6 0.4 - - - -
706A THR* 3.3 4.4 - - - -
707A HIS* 2.9 43.0 + - + -
709A ILE* 4.9 13.5 - - + -
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Residues in contact with GLU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 3.7 11.4 - - - -
147A THR* 3.6 24.2 + - - +
148A GLY* 3.8 8.1 - - - -
165A ARG* 2.9 44.5 + - - -
210A LYS* 3.4 21.4 + - - +
643A LYS 3.4 2.4 - - - +
644A VAL* 3.2 9.7 - - - +
645A ALA* 2.9 37.6 + - + +
647A PHE* 3.9 10.0 - - + -
688A LEU* 1.3 81.0 - - - +
690A TYR* 1.3 63.0 + - - +
691A GLN* 4.3 4.8 - - - +
705A TYR 3.4 3.8 - - - -
706A THR* 4.5 5.8 - - - -
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Residues in contact with TYR 690 (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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147A THR* 3.2 5.8 - - - +
643A LYS 3.8 2.0 - - - -
644A VAL* 3.6 34.1 - - + +
688A LEU* 3.3 40.6 - - + +
689A GLU* 1.3 73.7 - - - +
691A GLN* 1.3 61.5 + - - +
703A LEU* 4.7 10.1 - - + -
704A THR* 3.2 4.2 - - - -
705A TYR* 2.7 72.6 + + + +
707A HIS* 5.1 2.2 - - + -
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Residues in contact with GLN 691 (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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116A VAL* 4.9 1.6 - - - +
117A TYR* 4.3 21.0 + - + +
122A SER* 5.5 1.6 - - - +
123A VAL 4.3 11.9 + - - -
124A SER* 4.4 13.7 + - - -
147A THR* 2.6 31.9 + - - +
210A LYS* 4.0 2.8 + - - +
641A VAL 4.1 0.2 - - - +
642A ALA* 3.1 3.9 - - - -
643A LYS* 2.9 73.5 + - + +
644A VAL* 5.4 0.8 - - - +
689A GLU* 4.3 8.1 + - - +
690A TYR* 1.3 74.6 - - - +
692A LEU* 1.3 60.5 + - - +
703A LEU 3.2 9.9 - - - +
704A THR* 4.2 11.0 - - + -
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Residues in contact with LEU 692 (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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640A LEU* 3.7 26.7 - - + -
641A VAL 3.3 10.1 - - - +
642A ALA* 4.0 14.4 - - + -
691A GLN* 1.3 74.8 - - - +
693A ASN* 1.3 61.2 + - - +
694A TYR* 4.2 12.8 - - + +
701A ALA* 3.8 4.2 - - + +
702A ASP* 3.4 2.4 - - - +
703A LEU* 2.7 51.9 + - + +
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Residues in contact with ASN 693 (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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117A TYR* 4.7 8.5 + - + +
639A ARG* 3.0 41.6 + - - +
641A VAL* 2.7 42.3 + - + +
691A GLN 4.3 0.6 - - - -
692A LEU* 1.3 74.1 - - - +
694A TYR* 1.3 65.0 + - - +
695A ASP* 4.4 2.6 - - - +
700A TYR* 5.7 4.5 - - - +
701A ALA 3.3 4.0 + - - -
702A ASP* 2.7 38.6 + - - +
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Residues in contact with TYR 694 (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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633A LEU* 4.3 17.5 - - + -
634A TRP* 4.3 18.1 - + - +
635A PHE* 4.4 8.3 + - - -
638A ASP* 2.6 38.1 + - + -
639A ARG 3.1 23.6 - - - -
640A LEU* 4.2 15.3 - - + -
692A LEU* 4.2 7.7 - - + +
693A ASN* 1.3 75.4 - - - +
695A ASP* 1.3 61.9 + - - +
696A ALA* 3.3 26.3 - - + +
699A PHE* 4.3 26.5 - + - -
700A TYR* 3.2 4.2 - - - +
701A ALA* 2.7 48.2 + - + +
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Residues in contact with ASP 695 (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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638A ASP* 3.3 4.9 - - - +
639A ARG* 3.2 53.1 + - - +
693A ASN* 4.4 3.8 - - - +
694A TYR* 1.3 76.2 - - - +
696A ALA* 1.3 61.4 + - - +
697A GLY 3.3 4.8 + - - -
700A TYR* 3.4 12.4 - - + +
774A ARG* 3.2 35.1 + - - -
778A ARG* 4.6 6.6 + - - -
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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