Contacts of the strand formed by residues 689 - 693 (chain A) in PDB entry 6T8B
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 ILE 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A ASP* 5.3 2.9 - - + +
452A ILE* 4.9 16.6 - - + -
679A LEU 4.6 0.2 - - - -
680A TYR* 2.7 51.7 + - + +
682A PRO* 3.8 23.3 - - + -
685A THR* 5.8 2.5 - - + -
687A LEU* 3.0 11.3 + - + +
688A PRO* 1.3 68.9 - - - +
690A ARG* 1.3 62.0 + - - +
691A VAL* 3.5 19.3 + - + -
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Residues in contact with ARG 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.8 30.3 - - - +
398A ARG* 5.2 6.3 - - - +
412A GLU* 3.6 22.7 + - - +
446A ASP* 3.7 11.3 - - - +
447A ILE* 3.3 37.9 - - + +
671A GLN* 4.9 6.3 + - - +
672A LEU* 4.0 9.6 - - - +
673A LEU* 4.0 16.0 - - - +
677A ASP* 2.4 38.2 + - - +
678A MET 3.7 9.9 - - - +
679A LEU* 3.6 23.8 - - + -
688A PRO 3.2 5.9 + - - +
689A ILE* 1.3 72.1 - - - +
691A VAL* 1.3 65.2 + - - +
692A HIS* 4.0 6.7 - - + -
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Residues in contact with VAL 691 (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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443A LEU* 3.8 12.8 - - + -
444A GLY 3.7 29.2 - - - +
445A HIS 4.0 4.7 - - - +
446A ASP* 4.3 0.7 - - - +
452A ILE* 3.8 27.8 - - + -
677A ASP* 3.5 3.7 - - - +
678A MET* 2.9 48.3 + - + +
680A TYR* 4.2 10.3 - - + -
689A ILE* 3.5 19.6 + - + +
690A ARG* 1.3 78.6 - - - +
692A HIS* 1.3 74.7 + - - +
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Residues in contact with HIS 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.9 11.9 - - + +
364A VAL* 3.4 40.7 + - + +
365A ILE* 4.5 6.1 - - + +
418A ARG* 5.3 1.9 + - - +
421A VAL* 4.6 13.0 - - + +
444A GLY* 3.3 21.3 - - - -
445A HIS 2.8 28.7 + - - +
446A ASP 3.5 16.8 - - - -
447A ILE* 3.9 19.6 - - + +
676A GLY 3.9 3.1 - - - +
677A ASP* 3.1 30.4 + - - +
690A ARG* 4.0 13.9 - - - -
691A VAL* 1.3 75.5 - - - +
693A GLY* 1.3 70.5 + - - +
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Residues in contact with GLY 693 (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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421A VAL* 3.4 17.3 - - - +
443A LEU 4.0 6.3 - - - -
652A PHE* 5.5 0.4 - - - -
676A GLY* 2.5 27.4 + - - -
678A MET* 4.0 14.0 - - - +
691A VAL 4.0 1.2 + - - -
692A HIS* 1.3 77.5 - - - +
694A ALA* 1.3 57.5 + - - -
801A AGS 3.1 20.3 + - - -
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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