Contacts of the helix formed by residues 713 - 724 (chain B) in PDB entry 4PE5
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 GLY 713 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B VAL* 4.6 9.1 - - - +
711B GLN 3.7 5.7 + - - +
712B ARG* 1.3 74.8 - - - +
714B VAL* 1.3 62.0 + - - -
715B ASP* 3.4 10.3 - - - -
716B ASP* 3.6 4.8 + - - +
717B ALA* 3.1 26.9 + - - +
1G NAG 5.4 2.0 - - - +
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Residues in contact with VAL 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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413B GLU* 4.5 11.2 - - - +
686B VAL* 4.9 3.4 - - + -
713B GLY* 1.3 69.6 - - - -
715B ASP* 1.3 62.3 + - - +
717B ALA* 3.1 7.8 + - - +
718B LEU* 2.9 27.8 + - + +
729B PHE* 4.3 13.5 - - + -
731B TYR* 3.2 47.8 - - + +
735B VAL* 4.5 11.0 - - + -
736B LEU* 5.4 3.1 - - + -
739B MET* 5.5 15.3 - - + -
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Residues in contact with ASP 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B GLY* 4.0 2.6 - - - -
714B VAL* 1.3 81.0 + - - +
716B ASP* 1.3 88.6 + - - +
718B LEU* 3.2 8.4 + - - +
719B LEU* 2.9 37.8 + - + +
739B MET* 5.2 12.3 - - + +
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Residues in contact with ASP 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLN* 3.9 4.2 - - + +
712B ARG 3.2 26.4 - - - +
713B GLY* 3.9 2.5 - - - +
714B VAL 3.3 0.4 - - - -
715B ASP* 1.3 96.6 + - - +
717B ALA* 1.3 58.4 + - - +
719B LEU* 3.4 14.8 + - - +
720B SER* 2.9 27.9 + - - -
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Residues in contact with ALA 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLN* 3.3 17.0 + - + +
713B GLY 3.1 15.6 + - - +
714B VAL 3.1 8.9 + - - +
716B ASP* 1.3 76.0 - - - +
718B LEU* 1.3 58.2 + - - +
720B SER* 2.3 27.1 + - - +
721B LEU* 2.9 19.7 + - - +
726B LEU* 4.1 1.7 - - + +
729B PHE* 3.6 35.4 - - + -
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Residues in contact with LEU 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B MET* 6.2 2.5 - - + -
714B VAL* 2.9 13.6 + - + +
715B ASP* 3.2 10.5 + - - +
717B ALA* 1.3 78.3 - - - +
719B LEU* 1.3 61.7 + - + +
721B LEU* 3.1 15.8 + - + +
722B LYS* 2.9 27.5 + - + +
729B PHE* 5.2 3.8 - - + -
739B MET* 3.8 42.8 - - + +
743B ASP* 3.9 20.4 - - - +
748B LEU* 3.6 35.5 - - + +
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Residues in contact with LEU 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 ASP* 2.9 25.8 + - + +
716B ASP* 3.7 15.5 - - - +
717B ALA 3.3 0.2 - - - -
718B LEU* 1.3 79.7 - - + +
720B SER* 1.3 55.3 + - - +
722B LYS* 3.7 10.4 - - + +
723B THR* 2.6 38.9 + - - +
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Residues in contact with SER 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLN* 2.9 33.5 + - - -
716B ASP 2.9 10.3 + - - -
717B ALA* 2.3 24.7 + - - -
719B LEU* 1.3 73.6 - - - +
721B LEU* 1.3 63.6 + - - +
723B THR* 4.3 5.2 - - - -
724B GLY 3.1 18.7 + - - -
725B LYS* 3.3 17.7 + - - +
726B LEU* 3.3 18.3 + - - +
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Residues in contact with LEU 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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537B MET* 3.6 22.2 - - + +
539B SER* 4.4 16.6 - - - +
717B ALA 2.9 17.2 + - - +
718B LEU* 3.3 19.5 - - + +
720B SER* 1.3 79.7 + - - +
722B LYS* 1.3 61.0 + - - +
723B THR 3.5 0.3 + - - -
724B GLY* 3.8 6.9 + - - -
726B LEU* 3.3 35.8 - - + +
727B ASP 3.3 16.6 - - - +
728B ALA* 3.7 17.7 - - - -
729B PHE* 3.6 18.4 - - + -
748B LEU* 4.2 20.2 - - + -
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Residues in contact with LYS 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 LEU* 2.9 15.1 + - + +
719B LEU* 3.8 13.9 - - + +
720B SER 3.3 0.2 - - - -
721B LEU* 1.3 77.1 - - - +
723B THR* 1.3 65.3 + - - +
748B LEU* 5.3 12.1 - - + +
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Residues in contact with THR 723 (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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719B LEU* 2.6 22.2 + - - +
720B SER* 3.9 7.1 - - - -
722B LYS* 1.3 80.6 - - - +
724B GLY* 1.3 59.4 + - - +
725B LYS* 4.3 11.2 - - + +
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Residues in contact with GLY 724 (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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720B SER 3.1 4.9 + - - -
721B LEU 3.8 6.3 + - - -
722B LYS 3.6 1.2 - - - -
723B THR* 1.3 79.2 - - - +
725B LYS* 1.3 59.9 + - - +
726B LEU 3.2 9.6 + - - -
727B ASP* 5.2 2.3 - - - +
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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
------------------------------------------------------------
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