Contacts of the strand formed by residues 590 - 597 (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 VAL 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A TYR* 3.4 5.7 - - - -
587A TYR 2.9 34.9 + - - +
588A ASP* 3.9 7.6 - - + +
589A GLY* 1.3 84.0 - - - +
591A LEU* 1.3 62.1 + - - +
592A TYR* 3.5 39.9 - - + +
609A ARG* 3.8 23.8 - - + -
610A SER 3.5 8.5 - - - +
611A ARG* 4.4 15.9 - - + +
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Residues in contact with LEU 591 (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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530A ALA* 4.1 17.0 - - + -
532A ILE* 4.6 3.6 - - + -
538A ALA* 5.0 1.8 - - + -
553A LEU* 3.2 33.0 - - + -
584A ILE* 4.3 12.6 - - + -
585A LYS 3.5 20.4 - - - +
586A TYR* 3.8 16.9 - - + -
590A VAL* 1.3 72.2 - - - +
592A TYR* 1.3 62.3 + - - +
608A HIS 3.6 1.0 - - - +
609A ARG* 3.2 4.2 - - - -
610A SER* 2.9 43.3 + - - +
613A ILE* 3.8 36.6 - - + -
614A GLY 4.1 1.3 - - - +
617A TRP* 4.0 9.3 - - + -
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Residues in contact with TYR 592 (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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584A ILE* 3.3 7.0 - - - +
585A LYS 2.8 33.3 + - - +
587A TYR* 4.3 16.9 + + + -
590A VAL* 3.5 44.9 - - + +
591A LEU* 1.3 73.2 - - - +
593A LEU* 1.3 61.3 + - - +
607A LEU* 4.6 6.5 - - + -
608A HIS 3.3 5.8 - - - +
609A ARG* 4.0 23.7 + - + -
633A PHE* 3.6 22.4 - - + -
635A LYS* 3.7 35.5 - - + -
640A LEU* 4.0 19.5 - - + -
675A VAL* 3.9 24.2 - - + +
678A TRP* 4.5 2.5 - + - -
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Residues in contact with LEU 593 (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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551A VAL* 4.8 0.2 - - + -
552A GLY* 4.2 16.6 - - - +
553A LEU* 4.7 1.1 - - + -
571A ILE* 3.7 29.4 - - + -
582A PRO* 3.7 25.8 - - + -
583A CYS 3.3 3.4 - - - -
584A ILE* 3.6 24.2 - - + -
591A LEU 4.1 0.2 + - - -
592A TYR* 1.3 75.7 - - - +
594A ILE* 1.3 65.5 + - - +
595A THR* 3.8 21.1 - - + -
607A LEU* 3.4 3.2 - - - +
608A HIS* 2.8 40.6 + - + -
617A TRP* 4.0 24.7 - - + -
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Residues in contact with ILE 594 (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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581A GLU 4.1 0.9 - - - +
582A PRO* 3.3 1.4 - - - +
583A CYS* 2.9 36.0 + - + +
593A LEU* 1.3 78.3 - - - +
595A THR* 1.3 70.5 + - - +
606A SER 3.3 10.5 - - - +
607A LEU* 3.6 19.7 - - + -
622A PHE* 3.7 19.3 - - + -
631A LEU* 3.8 33.5 + - + +
633A PHE* 3.5 31.6 - - + -
640A LEU* 4.8 0.4 - - + -
642A MET* 3.7 30.7 - - + -
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Residues in contact with THR 595 (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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551A VAL* 4.0 12.1 - - + -
571A ILE* 3.9 22.2 - - + -
579A ALA* 4.1 13.4 - - + +
580A SER 4.0 6.1 - - - -
581A GLU 4.6 0.7 - - - -
582A PRO* 4.3 1.8 - - + -
593A LEU* 3.8 20.6 - - + -
594A ILE* 1.3 78.9 - - - +
596A ARG* 1.3 62.8 + - - +
604A GLY 4.3 1.7 + - - -
605A SER* 2.7 29.8 + - - -
606A SER* 3.0 35.9 + - - +
608A HIS* 4.5 0.4 - - - +
629A THR 4.7 0.7 - - - +
631A LEU* 4.4 6.2 - - - +
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Residues in contact with ARG 596 (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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330A GLN* 5.0 1.0 - - - +
579A ALA* 3.1 8.1 - - - +
580A SER* 2.9 50.9 + - - +
581A GLU* 2.8 35.5 + - - +
595A THR* 1.3 74.5 - - - +
597A GLY* 1.3 70.0 + - - +
598A THR* 5.4 3.4 - - - +
605A SER* 3.8 0.2 - - - -
628A HIS* 3.6 34.3 + - - +
629A THR 3.4 30.7 - - - +
630A THR* 4.1 9.6 - - + +
704A VAL* 3.8 18.6 - - - +
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Residues in contact with GLY 597 (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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578A ASP 3.4 7.9 - - - -
579A ALA* 4.6 0.4 - - - -
596A ARG* 1.3 81.2 + - - +
598A THR* 1.3 62.1 + - - -
599A ARG 3.6 2.2 - - - -
604A GLY* 4.2 7.2 - - - -
605A SER* 3.6 16.9 + - - +
626A VAL 3.7 15.8 + - - -
627A HIS* 3.9 4.3 - - - +
628A HIS* 2.9 23.7 + - - -
629A THR 4.5 0.4 + - - -
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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