Contacts of the strand formed by residues 639 - 645 (chain A) in PDB entry 3GVJ
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 ASP 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635A LYS* 3.3 6.7 - - - +
636A VAL 2.9 36.5 + - - +
637A GLY 3.2 0.2 - - - -
638A ASP* 1.3 81.5 - - - +
640A LEU* 1.3 67.0 + - - +
641A ILE* 3.8 3.0 + - + +
672A ARG* 2.9 46.8 + - + +
673A LEU 3.4 3.1 - - - +
674A ASN* 3.4 27.7 + - - +
675A VAL* 4.9 0.2 - - - -
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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
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592A TYR* 4.0 24.9 - - + -
594A ILE* 4.8 0.2 - - + -
607A LEU* 3.7 40.8 - - + -
633A PHE* 4.1 22.2 - - + -
634A ALA 3.4 3.6 - - - +
635A LYS* 3.9 27.1 - - + -
638A ASP 4.2 0.2 + - - -
639A ASP* 1.3 72.3 - - - +
641A ILE* 1.3 60.6 + - - +
642A MET* 3.9 17.7 - - + +
671A ALA 3.6 0.9 - - - +
672A ARG* 3.3 5.2 - - - -
673A LEU* 2.9 36.8 + - + +
675A VAL* 3.8 19.7 - - + -
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Residues in contact with ILE 641 (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 PHE* 3.2 20.4 - - - -
634A ALA 2.9 13.1 + - - +
636A VAL* 3.8 21.1 - - + -
639A ASP* 4.3 7.9 - - + +
640A LEU* 1.3 76.5 - - - +
642A MET* 1.3 59.4 + - - +
643A PHE* 4.0 18.1 - - + -
670A TYR* 3.9 29.6 - - + -
671A ALA 3.4 3.4 - - - +
672A ARG* 3.7 38.8 - - + +
714A ILE* 3.9 16.9 - - + +
752A MET* 4.9 1.6 - - - -
754A ILE* 3.7 19.5 - - + -
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Residues in contact with MET 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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594A ILE* 3.7 22.0 - - + -
607A LEU* 5.0 0.4 - - + -
622A PHE* 3.6 35.4 - - + -
631A LEU* 4.3 11.7 - - + +
632A PRO 3.5 9.6 - - - +
633A PHE* 3.9 6.3 - - + -
640A LEU* 4.1 26.5 - - + +
641A ILE* 1.3 74.9 - - - +
643A PHE* 1.3 64.0 + - - +
670A TYR* 3.2 7.1 - - - +
671A ALA 2.9 36.2 + - - +
673A LEU* 4.3 16.8 - - + -
683A ILE* 4.6 3.4 - - - -
685A TRP* 3.9 22.4 - - + -
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Residues in contact with PHE 643 (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 LEU* 3.4 11.7 - - - -
632A PRO* 3.1 32.7 + - - +
641A ILE* 4.0 19.1 - - + -
642A MET* 1.3 79.0 - - - +
644A GLY* 1.3 58.8 + - - +
668A THR* 5.4 0.2 - - + -
669A PHE 3.5 7.2 - - - -
670A TYR* 3.7 20.0 - - + -
685A TRP* 5.1 0.4 - - - -
688A ILE* 3.8 19.5 - - + -
707A VAL* 3.8 16.6 - - + -
714A ILE* 4.1 29.4 - - + -
716A TYR* 3.5 51.8 - + + -
750A TYR* 4.4 6.3 - + - -
752A MET* 4.0 20.9 - - + -
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Residues in contact with GLY 644 (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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629A THR* 3.4 13.2 - - - -
630A THR 3.9 0.2 - - - -
631A LEU* 3.9 11.3 - - - +
643A PHE* 1.3 75.2 - - - +
645A SER* 1.3 64.7 + - - -
652A TRP* 3.9 10.8 - - - -
668A THR* 3.5 2.1 - - - +
669A PHE 2.9 32.2 + - - +
685A TRP* 4.9 1.6 - - - -
716A TYR* 3.8 5.4 - - - -
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Residues in contact with SER 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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628A HIS 4.7 2.3 - - - +
629A THR* 3.1 23.3 + - - -
644A GLY* 1.3 72.5 - - - -
646A GLU* 1.3 69.2 + - - +
647A ALA* 3.7 1.0 + - - -
652A TRP* 3.8 6.6 - - - -
667A ARG 3.7 5.8 - - - -
668A THR* 2.8 25.4 + - - +
702A VAL* 4.2 6.4 - - - +
703A GLY* 3.7 25.3 - - - -
704A VAL 5.7 0.2 + - - -
716A TYR* 2.8 22.4 + - - -
718A PHE* 3.8 2.1 - - - -
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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