Contacts of the strand formed by residues 685 - 692 (chain r) in PDB entry 6FF7
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 685 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448r PRO 3.5 5.5 - - - +
449r ALA* 3.5 17.1 - - - +
450r LEU* 4.4 3.4 + - - +
681r ARG* 5.4 6.1 - - + +
683r VAL 3.5 5.1 + - - +
684r PRO* 1.3 74.2 - - - +
686r GLU* 1.3 62.4 + - - +
687r GLN* 3.7 5.8 + - + +
856r ALA* 5.8 7.6 - - + +
865r GLY 3.2 6.1 - - - +
866r GLU* 5.6 2.0 - - - -
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Residues in contact with GLU 686 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447r VAL 3.6 11.4 - - - +
448r PRO* 4.1 4.0 - - + -
449r ALA* 4.2 13.3 - - + +
685r LEU* 1.3 71.8 - - - +
687r GLN* 1.3 61.6 + - - +
688r THR* 3.8 0.7 + - - -
864r LYS* 6.4 0.4 - - + -
865r GLY 2.9 13.7 + - - +
866r GLU* 3.2 12.6 - - + +
867r GLY 3.0 25.3 + - - +
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Residues in contact with GLN 687 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445r VAL 3.9 0.9 - - - +
446r HIS* 3.6 3.1 - - - +
447r VAL* 2.9 50.3 + - + +
685r LEU* 3.7 7.4 + - + +
686r GLU* 1.3 71.2 - - - +
688r THR* 1.3 61.0 + - - +
689r TYR* 6.4 0.4 - - + -
867r GLY* 3.9 4.3 - - - +
883r LEU* 6.0 6.1 - - + -
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Residues in contact with THR 688 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445r VAL 3.6 5.4 - - - -
446r HIS* 4.9 2.0 - - - +
686r GLU 3.8 0.6 + - - -
687r GLN* 1.3 73.7 - - - +
689r TYR* 1.3 62.2 + - - +
690r VAL 4.2 0.2 - - - -
867r GLY 2.9 15.3 + - - +
868r ILE* 3.3 15.1 - - - -
869r LEU* 2.9 26.0 + - - +
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Residues in contact with TYR 689 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443r GLU 3.9 0.5 - - - +
444r GLU* 3.5 1.8 - - - -
445r VAL* 2.9 45.8 + - + +
687r GLN* 6.4 0.4 - - + -
688r THR* 1.3 76.9 - - - +
690r VAL* 1.3 59.6 + - - +
691r GLY 3.8 2.2 + - - +
869r LEU* 3.5 12.3 - - + +
876r LEU* 5.6 11.9 - - + +
879r TYR* 6.2 4.3 - - + -
880r LEU* 6.5 1.1 - - + -
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Residues in contact with VAL 690 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442r TYR* 5.2 7.0 - - + -
443r GLU 3.5 7.4 - - - +
444r GLU* 4.3 11.7 - - + +
688r THR 4.2 0.6 - - - -
689r TYR* 1.3 72.6 - - - +
691r GLY* 1.3 61.1 + - - +
692r ILE* 3.9 0.3 + - - +
707r ILE* 5.9 7.0 - - + -
869r LEU 2.9 12.5 + - - +
870r ILE* 3.6 8.9 - - + +
871r THR* 2.9 27.5 + - - +
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Residues in contact with GLY 691 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442r TYR* 3.1 6.1 - - - +
443r GLU* 2.9 35.7 + - - -
689r TYR 3.8 3.0 + - - -
690r VAL* 1.3 73.4 - - - +
692r ILE* 1.3 60.3 + - - -
871r THR* 3.3 7.9 - - - -
872r SER 4.0 1.8 - - - -
873r HIS* 3.6 21.7 - - - +
876r LEU* 4.4 12.5 - - - +
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Residues in contact with ILE 692 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441r GLY 3.4 8.1 - - - +
442r TYR* 3.9 6.3 - - + -
690r VAL 5.3 0.4 - - - +
691r GLY* 1.3 72.9 - - - -
693r THR* 1.3 62.5 + - - +
694r GLU* 3.3 12.1 + - + +
700r ARG* 5.8 6.5 - - + -
703r ILE* 5.9 7.2 - - + -
704r MET* 6.5 0.7 - - + -
871r THR 2.9 15.7 + - - +
872r SER* 4.1 5.6 - - - -
873r HIS* 3.1 19.5 + - - +
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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