Contacts of the strand formed by residues 714 - 719 (chain A) in PDB entry 6F3T
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 714 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A HIS* 3.7 12.8 - - - +
674A SER* 3.0 28.3 + - - +
687A GLY* 4.0 10.3 - - - -
688A ALA 3.2 6.4 + - - +
691A GLY* 3.7 33.0 - - - +
692A ARG 4.0 8.7 - - - +
693A VAL* 4.1 17.9 - - + -
710A HIS* 3.9 16.8 - - + -
712A ASP 4.1 0.9 - - - +
713A THR* 1.3 71.3 - - - +
715A CYS* 1.3 57.3 + - - +
716A SER 3.7 11.7 - - - +
717A LEU* 4.1 4.9 - - + -
728A SER* 4.2 5.4 - - - -
729A GLY 3.5 14.6 - - - +
730A SER* 4.2 0.7 - - - +
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Residues in contact with CYS 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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673A HIS* 4.0 18.2 - - + +
674A SER* 3.9 5.3 - - - -
713A THR* 4.6 7.9 - - + +
714A VAL* 1.3 72.8 - - - +
716A SER* 1.3 61.7 + - - +
729A GLY 2.9 10.9 + - - -
730A SER 3.9 2.0 - - - -
731A MET* 3.9 38.6 - - + -
779A PRO* 4.5 0.9 - - - -
780A VAL 3.5 22.9 - - - -
781A VAL* 3.8 21.8 - - + +
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Residues in contact with SER 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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674A SER* 3.7 4.5 - - - -
714A VAL* 3.6 2.6 - - - +
715A CYS* 1.3 80.1 - - - +
717A LEU* 1.3 72.5 + - - +
728A SER* 3.4 1.7 - - - -
729A GLY* 3.0 36.7 + - - +
780A VAL 3.0 15.3 + - - -
781A VAL 3.6 22.4 - - - -
782A HIS* 3.7 8.5 - - - -
783A LEU* 3.4 14.2 - - - +
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Residues in contact with LEU 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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674A SER* 3.4 28.5 - - - +
675A LEU 4.7 2.3 - - - +
676A THR* 3.7 19.4 - - + -
685A ALA* 3.5 29.4 - - + +
686A THR* 3.7 4.5 - - - -
687A GLY* 3.7 13.5 - - - +
693A VAL* 3.9 20.6 - - + -
714A VAL* 4.1 1.3 - - + -
716A SER* 1.3 82.3 - - - +
718A ARG* 1.3 79.3 + - - +
726A LEU* 4.3 9.2 - - + -
727A ALA 3.3 7.6 - - - +
728A SER* 3.6 22.4 - - - -
783A LEU* 4.5 3.9 + - - +
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Residues in contact with ARG 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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477A ASP* 5.3 1.8 + - - -
592A GLN* 6.0 0.6 - - - +
634A ARG* 4.9 19.2 - - - +
675A LEU 5.6 0.2 + - - -
676A THR* 4.0 20.6 + - - -
717A LEU* 1.3 81.4 + - - +
719A PHE* 1.3 73.4 + - - +
726A LEU* 3.8 5.5 - - - +
727A ALA* 2.7 40.7 + - - +
782A HIS* 3.4 32.5 + - - -
783A LEU* 2.8 37.6 + - + +
784A HIS* 4.7 2.1 - - - +
785A PHE* 3.7 20.8 - - + +
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Residues in contact with PHE 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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676A THR* 3.8 22.2 + - + -
677A PHE 3.3 19.7 - - - +
678A SER* 3.5 28.5 - - - -
679A PRO* 3.8 19.2 - - + +
683A PHE* 5.3 1.1 - - + -
685A ALA* 4.0 16.6 - - + -
695A LEU* 4.9 0.2 - - + -
718A ARG* 1.3 82.2 - - - +
720A SER* 1.3 64.7 + - - +
723A GLY* 4.5 8.5 - - - -
725A ILE 3.3 14.1 - - - -
726A LEU* 3.8 28.9 - - + -
740A ALA* 3.8 20.4 - - + -
744A PHE* 4.1 21.8 - + - -
785A PHE* 3.1 14.8 - - - +
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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