Contacts of the strand formed by residues 713 - 720 (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 TYR 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A GLN 6.2 0.4 - - - -
365A ASP* 6.3 0.9 - - + -
709A VAL* 3.4 5.4 - - - +
710A LYS 3.0 31.1 + - - +
711A ASP* 3.4 1.5 + - + -
712A ASN* 1.3 106.9 - - - +
714A ILE* 1.3 59.4 + - - +
715A TYR* 3.6 26.6 - - + +
751A LYS* 3.7 32.8 - - + -
752A MET* 3.4 5.2 - - - +
753A LYS* 3.5 41.9 - - + +
754A ILE* 3.9 3.8 - - - -
757A ASP* 2.8 25.2 + - - +
762A ARG* 4.3 9.0 + - - -
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Residues in contact with ILE 714 (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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634A ALA* 4.0 14.4 - - + -
636A VAL* 4.7 0.7 - - + -
641A ILE* 3.9 34.3 - - + +
643A PHE* 4.1 16.8 - - + -
707A VAL* 3.7 23.6 - - + -
708A VAL 3.4 11.4 - - - +
709A VAL* 3.9 10.1 - - + +
713A TYR* 1.3 75.9 - - - +
715A TYR* 1.3 65.2 + - - +
716A TYR 4.3 0.2 - - - -
750A TYR 3.6 0.9 - - - +
751A LYS* 3.6 3.3 - - - -
752A MET* 2.9 55.1 + - + +
754A ILE* 3.7 20.1 - - + +
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Residues in contact with TYR 715 (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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340A ILE* 3.6 24.0 - - + +
365A ASP* 3.1 38.7 + - - +
366A GLY* 4.3 4.3 - - - -
369A TRP* 5.3 0.4 - + - -
643A PHE* 5.3 0.4 - - - -
707A VAL* 3.2 9.2 - - - +
708A VAL* 2.8 57.3 + - + +
710A LYS* 4.0 16.1 + - + +
713A TYR* 3.6 33.3 - - + +
714A ILE* 1.3 76.2 - - - +
716A TYR* 1.3 60.4 + - - +
717A MET* 3.5 7.1 - - + +
749A CYS* 3.7 25.4 - - - -
750A TYR 3.4 3.6 - - - -
751A LYS* 3.6 28.9 - - + -
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Residues in contact with TYR 716 (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* 5.0 0.7 + - - -
630A THR 5.4 0.3 + - - -
632A PRO* 3.9 16.7 - - + +
643A PHE* 3.5 56.7 - + + -
644A GLY* 3.8 11.3 - - - -
645A SER* 2.8 26.1 + - - -
668A THR* 3.8 13.9 - - + -
703A GLY* 3.9 6.2 - - - -
704A VAL 4.6 1.4 + - - -
705A GLY* 4.2 6.6 + - - -
706A SER 3.6 4.7 - - - -
707A VAL* 3.9 11.7 - - + -
714A ILE 4.3 0.2 - - - -
715A TYR* 1.3 72.2 - - - +
717A MET* 1.3 62.9 + - - +
718A PHE* 3.3 53.0 - + + +
749A CYS* 3.2 3.0 - - - -
750A TYR* 2.8 41.5 + - + +
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Residues in contact with MET 717 (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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319A ILE* 4.2 7.0 - - + -
329A PRO* 3.6 13.5 - - + +
333A ALA* 3.7 22.7 - - + -
340A ILE* 4.2 19.1 - - - -
341A TYR 4.2 0.4 - - - +
342A ALA* 3.7 32.8 - - + -
369A TRP* 4.2 2.9 - - + -
705A GLY* 3.0 4.5 - - - -
706A SER* 2.9 50.6 + - - +
708A VAL* 3.9 19.3 - - + +
715A TYR* 3.5 19.7 - - + +
716A TYR* 1.3 69.7 - - - +
718A PHE* 1.3 61.7 + - - +
747A LEU* 5.7 0.4 - - + -
748A TYR 3.3 6.1 - - - +
749A CYS* 3.7 22.7 - - + -
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Residues in contact with PHE 718 (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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316A LEU* 3.8 24.5 - - + -
329A PRO* 3.9 11.7 - - - +
645A SER* 3.8 8.5 - - - -
668A THR* 3.6 9.4 - - - -
689A THR* 4.3 5.6 - - + -
691A GLN* 3.5 44.0 - - + -
703A GLY* 3.7 13.2 - - - +
705A GLY* 4.1 0.2 - - - -
716A TYR* 3.3 57.0 - + + +
717A MET* 1.3 76.5 - - - +
719A GLY* 1.3 77.5 + - - +
747A LEU* 3.5 3.9 - - - +
748A TYR* 2.8 44.0 + - + +
750A TYR* 4.0 3.6 - - + -
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Residues in contact with GLY 719 (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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326A ASN 5.0 0.2 - - - -
327A ALA* 5.2 2.2 - - - -
329A PRO* 4.4 3.2 - - - +
701A GLY 3.3 21.1 - - - -
702A VAL* 3.4 4.4 - - - +
703A GLY 3.0 29.6 + - - -
718A PHE* 1.3 86.4 - - - +
720A GLY* 1.3 58.7 + - - -
745A SER* 4.8 2.5 - - - -
746A ASP 3.5 8.3 - - - -
747A LEU* 4.4 6.3 - - - -
748A TYR* 4.3 1.8 - - - -
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Residues in contact with GLY 720 (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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691A GLN* 4.1 13.9 - - - -
701A GLY 4.0 0.8 + - - -
702A VAL* 4.2 7.2 - - - -
719A GLY* 1.3 74.5 - - - -
721A GLU* 1.3 65.8 + - - -
744A PRO 3.7 0.7 - - - +
745A SER* 3.5 2.2 + - - -
746A ASP 3.0 31.3 + - - +
748A TYR* 3.6 21.0 + - - -
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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