Contacts of the strand formed by residues 639 - 652 (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 ARG 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 5.6 5.4 - - - +
114A ASP* 2.8 33.9 + - - +
117A TYR* 5.2 1.0 - - - -
630A GLN 3.8 9.4 - - - +
631A PRO* 4.5 4.3 - - + -
638A ASP* 1.3 85.8 + - - +
640A LEU* 1.3 68.0 + - - +
641A VAL* 3.6 24.5 - - + +
693A ASN* 3.0 46.0 + - - +
694A TYR* 3.1 21.1 - - - -
695A ASP* 3.2 41.9 + - + +
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TRP* 4.7 9.2 - - + -
628A VAL* 3.9 18.1 - - + +
629A GLN* 3.7 0.7 - - - -
630A GLN* 3.0 39.6 + - + +
633A LEU* 3.6 43.6 - - + +
639A ARG* 1.3 75.6 - - - +
641A VAL* 1.3 78.3 + - - +
642A ALA* 5.6 1.1 - - + -
692A LEU* 3.7 37.9 - - + -
693A ASN 4.2 0.4 - - - -
694A TYR* 4.2 11.7 - - + -
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Residues in contact with VAL 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 4.5 5.6 - - - +
117A TYR* 3.4 46.0 - - + +
628A VAL 3.3 11.2 - - - +
629A GLN* 4.3 14.6 - - + +
639A ARG* 3.6 31.9 - - + +
640A LEU* 1.3 86.0 - - - +
642A ALA* 1.3 64.5 + - - +
692A LEU* 3.3 3.6 - - - +
693A ASN* 2.7 45.3 + - + +
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Residues in contact with ALA 642 (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* 3.5 6.9 - - - -
626A PHE* 6.0 0.9 - - + -
627A ASN* 3.2 6.8 - - - +
628A VAL* 2.8 46.5 + - + +
640A LEU* 5.5 1.8 - - + -
641A VAL* 1.3 77.5 - - - +
643A LYS* 1.3 62.2 + - - +
644A VAL* 5.7 4.7 - - + -
691A GLN 3.1 12.6 - - - +
692A LEU* 4.0 21.8 - - + -
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Residues in contact with LYS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.1 33.7 + - - +
117A TYR* 3.9 10.1 - - + -
119A GLU 3.6 3.2 + - - -
121A ARG 2.5 30.6 + - - +
122A SER* 4.2 11.2 - - - -
123A VAL* 3.9 5.3 + - - +
581A TYR* 4.5 7.2 - - - +
626A PHE* 3.3 13.0 - - - +
627A ASN* 3.6 22.7 - - + +
642A ALA* 1.3 78.8 - - - +
644A VAL* 1.3 69.3 + - - +
645A ALA* 5.0 2.5 - - + -
689A GLU 3.4 4.2 - - - +
691A GLN* 2.9 61.5 + - + +
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A TYR* 4.5 0.2 + - - -
625A GLY* 3.2 2.6 - - - -
626A PHE* 3.0 66.3 + - + +
642A ALA* 5.7 3.4 - - + -
643A LYS* 1.3 80.9 - - - +
645A ALA* 1.3 69.0 + - - +
688A LEU* 5.0 7.0 - - + -
689A GLU 3.2 5.2 - - - +
690A TYR* 3.6 43.5 - - + -
691A GLN 5.4 0.4 - - - +
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Residues in contact with ALA 645 (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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122A SER* 4.4 9.9 - - - -
165A ARG* 5.3 1.1 - - - +
581A TYR* 3.5 9.4 - - - +
623A GLU* 3.3 27.8 - - - +
624A VAL 3.4 5.6 - - - +
643A LYS* 5.0 3.8 - - + -
644A VAL* 1.3 79.1 - - - +
646A TYR* 1.3 59.4 + - - +
647A PHE* 4.2 1.1 + - - -
687A GLY 3.8 0.5 - - - +
688A LEU* 3.3 8.8 - - - +
689A GLU* 2.9 43.4 + - + +
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Residues in contact with TYR 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A TRP* 4.1 2.0 - - + +
623A GLU* 3.2 4.5 - - - +
624A VAL* 2.7 54.6 + - + +
645A ALA* 1.3 73.4 - - - +
647A PHE* 1.3 73.5 + - - +
648A ASP* 4.3 16.3 - - + +
684A ARG* 5.5 0.2 + - - -
686A ARG* 3.7 26.6 + - + -
687A GLY* 3.3 22.4 - - - -
688A LEU* 3.6 21.3 - - + -
709A ILE* 4.8 11.0 - - + -
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 3.5 72.9 - - + +
622A TRP 3.3 8.3 - - - +
623A GLU* 4.6 6.5 - - + +
645A ALA 4.6 2.0 - - - -
646A TYR* 1.3 80.0 - - - +
648A ASP* 1.3 62.5 + - - +
649A THR* 4.5 6.1 - - - +
685A PHE* 3.7 12.8 - - + -
686A ARG* 3.2 26.0 - - - +
687A GLY* 3.1 58.6 + - - +
688A LEU 3.9 2.5 - - - -
689A GLU* 3.9 16.8 - - + -
706A THR* 6.4 0.4 - - - -
707A HIS 6.1 0.2 - - - -
708A MET* 4.0 14.6 - - + -
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Residues in contact with ASP 648 (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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620A ARG 3.6 3.3 - - - +
621A ALA* 3.4 1.6 - - - -
622A TRP* 2.7 55.0 + - + +
646A TYR* 4.3 18.6 - - + +
647A PHE* 1.3 76.0 - - - +
649A THR* 1.3 62.7 + - - +
650A LYS* 5.3 2.8 - - - +
684A ARG* 3.2 45.5 + - - +
685A PHE 3.6 1.6 - - - -
686A ARG* 3.5 13.9 - - - +
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Residues in contact with THR 649 (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* 5.1 6.2 + - - -
167A ILE* 4.2 16.2 - - + +
211A GLY* 5.4 4.3 - - - -
212A THR* 5.2 0.4 - - + -
222A LEU 4.7 6.3 - - - +
619A SER* 4.4 9.4 - - - -
620A ARG 4.0 1.8 - - - -
621A ALA* 3.9 21.1 - - + +
647A PHE* 4.5 9.5 - - - +
648A ASP* 1.3 74.8 + - - +
650A LYS* 1.3 62.1 + - - +
651A VAL* 3.9 20.6 - - + -
683A THR 3.7 1.4 - - - +
684A ARG* 3.4 4.3 - - - +
685A PHE* 2.6 52.6 + - - +
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Residues in contact with LYS 650 (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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618A ARG 4.1 0.5 - - - +
619A SER* 3.3 2.6 - - - -
620A ARG* 2.9 59.0 + - + +
648A ASP* 4.0 3.3 + - - +
649A THR* 1.3 72.8 - - - +
651A VAL* 1.3 64.2 + - - +
652A ASP 4.3 0.2 + - - -
682A LYS* 4.0 40.7 + - + +
683A THR 3.6 6.1 - - - +
684A ARG* 4.2 30.5 - - + +
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Residues in contact with VAL 651 (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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167A ILE* 4.7 0.4 - - + -
222A LEU* 4.0 23.1 - - + -
617A GLU* 4.0 9.4 - - + -
618A ARG 3.6 12.1 - - - +
619A SER* 3.7 14.6 - - - -
649A THR* 3.9 15.3 - - + -
650A LYS* 1.3 78.5 - - - +
652A ASP* 1.3 73.4 + - - +
654A TYR* 3.9 24.0 - - + -
682A LYS* 3.8 3.4 - - - -
683A THR* 2.8 48.2 + - - +
685A PHE* 4.3 12.1 - - + -
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Residues in contact with ASP 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A GLU* 3.8 0.3 - - - -
618A ARG* 2.9 37.1 + - - +
620A ARG* 5.9 1.2 + - - -
650A LYS 4.3 0.2 - - - -
651A VAL* 1.3 76.4 - - - +
653A ASN* 1.3 88.4 + - - +
654A TYR 3.1 4.0 + - - +
681A SER 4.5 6.1 - - - +
682A LYS* 2.8 39.0 + - + +
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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