Contacts of the helix formed by residues 710 - 722 (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 ASN 710 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709B TRP* 1.3 82.1 - - - +
711B ARG* 1.3 66.6 + - - +
712B LYS* 3.5 2.5 - - + +
713B LYS* 4.2 19.3 - - + +
714B LEU* 3.5 17.8 + - - +
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Residues in contact with ARG 711 (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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709B TRP 4.0 0.6 + - - -
710B ASN* 1.3 74.4 - - - +
712B LYS* 1.3 59.5 + - - +
713B LYS 3.4 0.2 + - - -
714B LEU* 4.0 1.8 - - - +
715B GLY* 3.0 25.1 + - - -
730B ARG* 4.7 19.2 - - + +
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Residues in contact with LYS 712 (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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710B ASN* 3.5 2.9 - - + +
711B ARG* 1.3 79.0 - - - +
713B LYS* 1.3 57.2 + - - +
715B GLY* 3.7 1.8 - - - +
716B GLU* 2.8 30.8 + - - +
730B ARG* 4.9 9.9 - - + -
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Residues in contact with LYS 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B TRP* 5.3 3.6 - - + -
710B ASN* 3.8 23.2 + - + +
711B ARG 3.3 0.8 - - - -
712B LYS* 1.3 78.0 - - - +
714B LEU* 1.3 59.3 + - - +
716B GLU* 3.3 6.5 + - - +
717B PHE* 2.9 26.2 + - - +
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Residues in contact with LEU 714 (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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705B VAL* 5.4 12.6 - - + -
706B GLN 5.4 3.4 - - - +
709B TRP* 4.7 12.3 - - + +
710B ASN 3.5 14.0 + - - +
711B ARG 4.4 1.3 - - - +
713B LYS* 1.3 75.6 - - - +
715B GLY* 1.3 60.7 + - - +
717B PHE* 3.6 8.4 - - + +
718B PHE* 2.9 30.3 + - - +
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Residues in contact with GLY 715 (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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711B ARG 3.0 19.1 + - - -
712B LYS* 3.7 2.5 - - - -
713B LYS 3.2 0.2 - - - -
714B LEU* 1.3 77.4 - - - +
716B GLU* 1.3 56.3 + - - +
718B PHE* 3.8 2.1 - - - -
719B GLN* 2.9 30.0 + - - +
729B ALA* 3.7 31.0 - - - +
730B ARG* 4.4 5.4 - - - -
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Residues in contact with GLU 716 (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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712B LYS 2.8 21.1 + - - +
713B LYS* 3.7 6.3 - - - +
715B GLY* 1.3 70.2 - - - +
717B PHE* 1.3 59.8 + - - +
719B GLN* 3.4 7.4 - - - +
720B THR* 2.9 31.5 + - - -
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Residues in contact with PHE 717 (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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713B LYS 2.9 16.5 + - - +
714B LEU* 3.6 10.8 - - - +
715B GLY 3.3 0.2 - - - -
716B GLU* 1.3 77.7 - - - +
718B PHE* 1.3 55.3 + - - +
720B THR* 3.8 2.8 - - - -
721B LYS* 3.0 32.2 + - - +
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Residues in contact with PHE 718 (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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714B LEU 2.9 17.4 + - - +
715B GLY* 3.9 5.4 - - - +
717B PHE* 1.3 76.3 - - - +
719B GLN* 1.3 56.8 + - - +
721B LYS* 4.5 4.7 - - - -
722B TYR* 2.9 35.8 + - + +
724B TRP* 4.4 6.2 - - + +
729B ALA* 5.2 7.9 - - + +
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Residues in contact with GLN 719 (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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715B GLY 2.9 19.8 + - - +
716B GLU* 3.4 11.4 - - - +
718B PHE* 1.3 76.1 - - - +
720B THR* 1.3 58.3 + - - +
723B ASP* 3.2 30.1 + - - -
724B TRP* 3.6 16.2 + - - +
725B ASP 5.6 0.4 - - - +
726B LEU* 5.9 3.8 - - - -
729B ALA* 4.5 9.4 - - + +
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Residues in contact with THR 720 (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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716B GLU 2.9 19.4 + - - -
717B PHE* 4.3 2.5 - - - -
719B GLN* 1.3 72.3 - - - +
721B LYS* 1.3 59.4 + - - +
723B ASP* 4.6 1.9 + - - -
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Residues in contact with LYS 721 (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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717B PHE 3.0 19.0 + - - +
718B PHE* 4.1 4.5 - - - +
719B GLN 3.2 0.2 - - - -
720B THR* 1.3 80.1 - - - +
722B TYR* 1.3 59.4 + - + +
723B ASP* 3.5 1.8 + - - +
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Residues in contact with TYR 722 (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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718B PHE* 2.9 16.8 + - + +
721B LYS* 1.3 77.2 - - + +
723B ASP* 1.3 57.1 + - - +
724B TRP* 2.9 22.5 + - + +
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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