Contacts of the strand formed by residues 702 - 707 (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 LEU 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A ARG* 3.2 34.3 - - - +
665A PHE* 4.2 0.2 - - - -
696A TRP* 3.4 8.6 - - - +
697A ASP* 2.8 31.4 + - - +
700A HIS* 3.8 21.5 - - + +
701A GLY* 1.3 75.7 - - - +
703A MET* 1.3 69.2 + - - +
704A VAL* 4.6 6.3 - - + -
754A THR* 4.9 9.9 - - - +
755A ALA 5.8 0.4 - - - +
757A GLY 2.8 35.2 - - - +
758A HIS* 3.8 3.1 - - - +
759A ILE* 4.0 26.2 - - + -
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Residues in contact with MET 703 (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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354A ALA* 3.3 34.8 - - - +
355A MET* 3.7 28.7 - - - +
666A THR 4.1 1.3 - - - +
694A LEU* 4.0 22.4 - - + -
695A LEU 3.5 7.9 - - - +
696A TRP* 3.7 34.2 - - + -
702A LEU* 1.3 74.5 - - - +
704A VAL* 1.3 60.0 + - - +
705A GLY 3.8 17.9 - - - +
706A GLU* 4.6 0.2 - - - -
759A ILE* 3.5 16.8 - - - +
761A LEU* 3.4 38.5 - - + +
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A PHE* 4.5 0.9 - - + -
695A LEU* 2.8 30.7 + - + +
696A TRP 4.2 0.9 - - - +
697A ASP* 3.7 31.0 - - + +
700A HIS* 6.1 0.4 - - - +
702A LEU* 3.9 5.6 - - + +
703A MET* 1.3 78.2 - - - +
705A GLY* 1.3 58.2 + - - +
743A ALA 4.5 9.9 - - - +
744A PHE* 4.0 16.8 - - + -
747A LEU* 4.0 28.3 - - + +
759A ILE* 4.1 17.9 - - + +
761A LEU* 3.8 10.8 - - - +
762A PRO* 4.8 8.1 - - - +
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Residues in contact with GLY 705 (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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694A LEU* 3.4 4.0 - - - -
695A LEU* 2.8 45.7 + - - -
703A MET* 3.7 7.6 - - - +
704A VAL* 1.3 80.3 - - - +
706A GLU* 1.3 60.7 + - - +
707A LEU* 4.1 2.7 - - - -
743A ALA* 6.2 0.2 - - - -
761A LEU* 3.9 9.2 - - - +
762A PRO* 5.7 2.2 - - - -
768A LEU* 6.1 2.2 - - - -
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Residues in contact with GLU 706 (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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350A GLN* 5.6 3.3 - - - +
354A ALA* 3.8 17.4 - - - +
692A ARG* 2.6 30.4 + - - +
693A VAL 3.7 2.9 - - - -
694A LEU* 3.8 17.3 - - + -
705A GLY* 1.3 73.3 - - - +
707A LEU* 1.3 63.5 + - - +
708A LYS* 3.5 42.1 + - + +
761A LEU* 3.5 21.8 - - + +
762A PRO* 5.2 8.9 + - - +
763A GLU* 4.5 4.5 - - - +
765A SER* 3.0 17.2 + - - -
768A LEU* 5.9 0.2 - - - +
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Residues in contact with LEU 707 (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 GLY 4.3 1.6 - - - +
692A ARG* 3.7 4.8 - - - -
693A VAL* 2.7 48.6 + - + +
695A LEU* 4.1 24.9 - - + -
705A GLY* 5.3 0.2 - - - -
706A GLU* 1.3 76.1 - - - +
708A LYS* 1.3 61.7 + - - +
709A GLY 4.1 0.9 + - - -
710A HIS* 6.0 0.3 - - - -
726A LEU* 3.9 22.0 - - + -
738A TRP* 3.7 52.4 - - + -
743A ALA* 5.4 0.9 - - + -
765A SER* 3.8 3.8 - - - +
768A LEU* 3.4 33.9 - - + -
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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