Contacts of the helix formed by residues 693 - 702 (chain B) 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 GLU 693 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692B LEU* 1.3 78.1 - - - +
694B LYS* 1.3 65.3 + - - +
695B GLY 3.3 4.2 + - - +
696B LEU* 3.6 12.1 + - + +
697B ALA* 3.1 21.4 + - - +
786B ASN* 6.5 0.4 - - - -
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Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B LEU 4.2 1.0 + - - -
693B GLU* 1.3 71.4 - - - +
695B GLY* 1.3 60.2 + - - +
697B ALA* 3.5 8.5 - - - +
698B GLU* 2.9 28.2 + - - +
786B ASN* 6.2 2.5 - - - -
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Residues in contact with GLY 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693B GLU* 3.3 2.2 - - - +
694B LYS* 1.3 79.1 - - - +
696B LEU* 1.3 57.1 + - - +
698B GLU* 3.2 8.7 + - - +
699B ASP* 2.9 25.7 + - - +
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693B GLU* 3.6 13.9 + - + +
694B LYS 3.5 0.2 - - - -
695B GLY* 1.3 73.1 - - - +
697B ALA* 1.3 59.8 + - - +
699B ASP* 3.5 10.3 - - + +
700B ILE* 2.9 30.1 + - - +
721B LYS* 6.4 2.0 - - + -
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Residues in contact with ALA 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B LEU* 5.3 4.2 - - + +
693B GLU 3.1 18.9 + - - +
694B LYS* 3.5 10.1 - - - +
695B GLY 3.2 0.2 - - - -
696B LEU* 1.3 76.7 - - - +
698B GLU* 1.3 58.3 + - - +
700B ILE* 3.9 1.3 - - - +
701B GLU* 2.9 28.4 + - - +
742B PRO* 3.8 29.8 - - + +
786B ASN* 5.1 13.9 - - + -
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Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694B LYS 2.9 14.4 + - - +
695B GLY* 3.2 10.5 + - - +
697B ALA* 1.3 75.4 - - - +
699B ASP* 1.3 59.0 + - - +
701B GLU* 3.4 8.1 + - - +
702B ASN* 2.9 30.4 + - - +
903B HIS* 6.1 5.2 - - + -
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Residues in contact with ASP 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B GLY 2.9 14.1 + - - +
696B LEU* 3.5 13.9 - - + +
697B ALA 3.2 0.2 - - - -
698B GLU* 1.3 75.0 - - - +
700B ILE* 1.3 61.1 + - - +
702B ASN* 3.1 18.0 + - - +
704B VAL* 3.2 36.1 + - + +
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Residues in contact with ILE 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B LEU 2.9 16.0 + - - +
697B ALA* 4.3 4.3 - - - +
699B ASP* 1.3 75.4 - - - +
701B GLU* 1.3 60.7 + - - +
703B GLU* 3.7 10.0 + - - +
704B VAL 4.8 2.7 - - - +
705B VAL* 5.1 15.4 - - + +
740B THR* 2.9 28.9 - - - +
741B GLY 5.5 0.2 - - - -
742B PRO* 5.2 8.5 - - + -
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Residues in contact with GLU 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697B ALA 2.9 19.6 + - - +
698B GLU* 3.6 10.1 - - - +
699B ASP 3.2 0.2 - - - -
700B ILE* 1.3 78.5 - - - +
702B ASN* 1.3 56.9 + - + +
703B GLU* 3.3 3.9 + - - +
740B THR* 3.9 12.6 + - - -
741B GLY* 5.4 3.8 - - - -
742B PRO 5.5 0.2 - - - -
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Residues in contact with ASN 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B GLU 2.9 16.4 + - - +
699B ASP* 3.1 5.9 + - - +
701B GLU* 1.3 75.7 - - + +
703B GLU* 1.3 66.0 + - - +
704B VAL* 3.1 6.9 + - + +
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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