Contacts of the strand formed by residues 715 - 720 (chain A) in PDB entry 5HQG
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 715 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A LEU* 4.5 6.7 - - + -
450A TYR* 3.6 14.8 - - + +
705A TRP* 4.0 7.1 - - - -
706A ARG* 3.2 52.4 + - + +
712A GLU 5.4 2.7 - - - +
713A SER 3.4 0.7 - - - -
714A ASN* 1.3 84.1 - - + +
716A LEU* 1.3 68.5 + - - +
717A ILE* 5.6 0.2 - - + -
727A VAL* 3.6 27.6 - - + -
728A LEU 3.1 15.9 - - - +
729A GLU* 4.5 6.5 - - + +
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Residues in contact with LEU 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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656A ALA* 4.2 15.9 - - + -
664A LEU* 3.9 22.2 - - + -
666A LEU* 5.0 2.9 - - + -
703A VAL* 4.3 5.2 - - + -
704A CYS 3.1 16.8 - - - +
705A TRP* 3.7 44.2 - - + -
706A ARG* 4.2 3.8 - - - +
715A VAL* 1.3 77.9 - - - +
717A ILE* 1.3 70.1 + - - +
727A VAL* 3.6 2.1 - - - -
728A LEU* 2.8 50.7 + - + +
730A LEU* 5.0 13.5 - - + -
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Residues in contact with ILE 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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427A ILE* 3.9 23.7 - - + +
429A PHE* 3.4 35.0 - - + -
436A PHE* 3.6 34.1 - - + -
450A TYR* 4.7 1.8 - - + -
703A VAL* 3.3 3.3 - - - +
704A CYS 2.9 33.5 + - - +
715A VAL* 5.6 0.2 - - + -
716A LEU* 1.3 80.4 - - - +
718A ALA* 1.3 62.1 + - - +
725A ILE* 3.6 28.3 - - + -
726A LYS 3.4 7.9 - - - +
727A VAL* 3.9 22.2 - - + -
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Residues in contact with ALA 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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427A ILE* 4.0 2.9 - - - -
664A LEU* 4.0 25.6 - - + -
680A PHE* 3.7 21.8 - - + -
700A VAL* 4.5 7.4 - - + -
702A ALA 3.2 11.7 - - - +
703A VAL* 4.5 3.6 - - + -
716A LEU* 4.9 0.6 - - - +
717A ILE* 1.3 74.1 - - - +
719A ALA* 1.3 61.3 + - - +
725A ILE* 3.5 2.4 - - - +
726A LYS 2.9 33.2 + - - +
728A LEU* 4.6 4.3 - - + -
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Residues in contact with ALA 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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424A VAL* 3.5 36.8 - - + -
427A ILE* 3.8 8.9 - - + +
680A PHE* 4.4 2.2 - - - -
700A VAL* 3.3 7.4 - - - +
701A SER* 2.8 22.4 + - - +
702A ALA* 3.0 11.6 + - + +
718A ALA* 1.3 76.3 - - - +
720A ASN* 1.3 61.5 + - - +
724A THR 3.1 13.5 - - - +
725A ILE* 3.9 10.5 - - + -
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Residues in contact with ASN 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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424A VAL 4.0 6.2 + - - -
662A ASN* 3.2 27.8 + - - +
680A PHE* 4.1 17.3 - - + +
681A ASP 4.6 1.4 + - - -
698A GLU* 4.6 2.2 - - - +
699A PHE 3.2 15.5 - - - +
700A VAL* 4.1 2.5 - - - -
701A SER* 3.5 11.6 + - - -
719A ALA* 1.3 74.0 - - - +
721A SER* 1.3 60.7 + - - +
722A GLN* 3.1 30.6 + - - +
723A GLY* 3.0 15.6 + - - -
724A THR* 2.8 43.9 + - - -
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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