Contacts of the strand formed by residues 683 - 688 (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 PHE 683 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A PHE* 3.7 5.4 - - - +
678A SER* 3.0 37.8 + - - +
680A ASN* 3.9 10.1 - - - -
681A GLY 3.5 0.4 - - - -
682A ARG* 1.3 129.8 + - + +
684A LEU* 1.3 63.2 + - - +
696A TRP 3.2 15.0 - - - +
697A ASP* 3.9 18.2 - - + -
698A ILE* 3.8 9.2 - - - +
704A VAL* 4.5 0.7 - - + -
719A PHE* 5.3 0.7 - - + -
744A PHE* 3.4 66.0 - + + -
747A LEU* 3.4 25.4 - - + -
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Residues in contact with LEU 684 (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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643A ALA* 4.3 10.1 - - + -
651A VAL* 3.9 28.0 - - + -
652A ARG 5.8 0.2 - - - +
653A LEU* 5.3 3.8 - - + -
665A PHE* 4.1 20.0 - - + -
675A LEU* 3.9 15.3 - - + -
676A THR 3.3 26.0 - - - +
677A PHE* 3.8 26.9 - - + -
678A SER 4.9 0.2 - - - +
683A PHE* 1.3 76.2 - - - +
685A ALA* 1.3 59.6 + - - +
686A THR* 4.1 8.5 - - + -
695A LEU* 3.5 2.6 - - - -
696A TRP* 2.8 48.1 + - + +
698A ILE* 4.4 10.5 - - + -
719A PHE* 5.2 1.1 - - - -
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Residues in contact with ALA 685 (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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675A LEU* 3.5 1.2 - - - -
676A THR* 2.8 39.0 + - + +
684A LEU* 1.3 73.2 - - - +
686A THR* 1.3 67.6 + - - +
693A VAL* 4.3 1.6 - - + -
694A LEU 3.4 4.9 - - - +
695A LEU* 3.8 21.5 - - + -
717A LEU* 3.5 7.7 - - + +
719A PHE* 4.0 21.0 - - + -
726A LEU* 4.0 11.9 - - + -
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Residues in contact with THR 686 (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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651A VAL* 3.8 30.4 - - + +
668A HIS* 2.9 27.0 + - - -
672A ILE* 4.6 1.6 - - - -
674A SER 3.5 7.6 - - - -
675A LEU* 3.9 19.1 - - + -
684A LEU* 4.1 4.9 - - + -
685A ALA* 1.3 80.1 - - - +
687A GLY* 1.3 58.4 + - - +
693A VAL* 3.3 4.3 - - - -
694A LEU 2.9 29.8 + - - -
696A TRP* 2.8 30.8 + - + +
717A LEU* 3.7 5.4 - - - -
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A HIS* 3.7 2.7 - - - -
672A ILE* 3.5 3.8 - - - +
673A HIS 3.0 21.7 + - - -
674A SER* 3.1 30.8 + - - +
686A THR* 1.3 74.7 - - - +
688A ALA* 1.3 60.9 + - - -
692A ARG 3.4 11.0 - - - -
693A VAL* 4.6 0.4 - - - -
714A VAL* 4.0 13.7 - - - -
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Residues in contact with ALA 688 (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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668A HIS* 3.3 31.0 - - + +
670A GLY 3.4 16.4 - - - +
671A PRO 3.1 19.1 - - - +
672A ILE* 3.9 1.6 - - + -
673A HIS 4.1 2.0 - - - +
687A GLY* 1.3 73.2 - - - +
689A THR* 1.3 63.8 + - - +
690A ASP* 3.0 9.5 + - - +
691A GLY* 3.1 10.9 + - - -
692A ARG 3.7 2.6 + - - -
713A THR* 4.0 6.3 - - - -
714A VAL 3.2 14.6 + - - -
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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