Contacts of the helix formed by residues 715 - 724 (chain B) in PDB entry 3A8P
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 SER 715 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676B ARG* 4.8 6.8 + - - -
679B GLU* 3.8 29.8 - - - -
683B GLU* 2.8 18.9 + - - -
713B ALA 3.1 5.1 + - - -
714B THR* 1.3 76.2 - - - +
716B ARG* 1.3 65.5 + - - +
717B PRO* 3.3 12.6 - - - +
718B SER* 2.9 29.1 + - - -
719B LYS* 2.9 21.5 + - - +
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Residues in contact with ARG 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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581A LYS* 4.5 13.3 + - - +
583A GLU* 4.1 35.9 + - + +
679B GLU* 5.1 1.6 + - - -
715B SER* 1.3 72.3 - - - +
717B PRO* 1.3 73.0 - - + +
719B LYS* 3.2 7.4 + - - +
720B LEU* 2.9 69.0 + - + +
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Residues in contact with PRO 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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676B ARG* 4.3 30.7 - - - +
679B GLU* 4.7 5.6 - - - +
715B SER* 3.3 14.6 - - - +
716B ARG* 1.3 95.9 - - + +
718B SER* 1.3 56.3 + - - +
720B LEU* 3.1 12.9 + - + +
721B ALA* 2.8 29.3 + - - +
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Residues in contact with SER 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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676B ARG* 5.8 0.7 + - - -
683B GLU* 2.6 30.3 + - - -
714B THR* 3.8 10.5 - - - -
715B SER* 2.9 8.9 + - - -
717B PRO* 1.3 76.9 - - - +
719B LYS* 1.3 64.7 + - - +
721B ALA* 3.0 5.2 + - - +
722B LEU* 2.9 27.9 + - - +
733B PHE* 4.6 0.9 - - - -
736B LEU* 3.5 20.0 - - - -
740B ARG* 2.8 22.8 + - - +
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Residues in contact with LYS 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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577A PRO 3.4 20.8 + - - +
578A GLU* 4.4 2.9 - - - +
579A HIS 2.7 23.8 + - - -
580A PRO* 4.4 11.7 - - + +
582A LYS 2.6 32.1 + - - +
583A GLU* 2.7 38.5 + - - +
714B THR* 3.8 13.9 - - + +
715B SER 2.9 14.0 + - - +
716B ARG* 3.2 9.6 + - + +
718B SER* 1.3 78.5 - - - +
720B LEU* 1.3 64.4 + - + +
722B LEU* 3.3 6.6 + - - +
723B GLY* 3.2 18.7 + - - -
728B LEU* 4.8 16.3 - - + +
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Residues in contact with LEU 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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580A PRO 4.5 16.2 - - - +
581A LYS* 6.1 3.1 - - + -
583A GLU* 5.9 0.9 - - - +
716B ARG* 2.9 61.8 + - + +
717B PRO* 3.1 10.1 + - + +
719B LYS* 1.3 78.6 - - + +
721B ALA* 1.3 63.8 + - - +
723B GLY* 3.2 13.8 + - - +
724B ARG* 4.3 2.6 + - - +
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Residues in contact with ALA 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 PRO 2.8 13.6 + - - +
718B SER* 3.4 12.1 - - - +
720B LEU* 1.3 78.3 - - - +
722B LEU* 1.3 62.4 + - - +
723B GLY 3.5 0.5 + - - -
724B ARG* 3.6 27.4 + - - +
725B LEU* 5.1 0.7 - - - +
736B LEU* 4.7 15.3 - - + -
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Residues in contact with LEU 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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525B LEU* 4.3 7.2 - - + -
714B THR* 4.7 0.9 - - + -
718B SER 2.9 21.7 + - - +
719B LYS 3.8 3.6 - - - +
720B LEU 3.3 0.2 - - - -
721B ALA* 1.3 74.6 - - - +
723B GLY* 1.3 65.6 + - - +
724B ARG 3.3 1.3 - - - -
725B LEU* 3.0 31.7 + - + +
726B GLY 3.2 11.8 - - - +
727B VAL 5.2 0.3 - - - -
728B LEU* 3.3 37.2 - - + -
732B SER* 3.5 31.4 - - - +
733B PHE* 3.7 22.9 - - + +
736B LEU* 3.9 24.7 - - + -
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Residues in contact with GLY 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 LYS 3.2 12.2 + - - -
720B LEU* 3.2 9.7 + - - -
722B LEU* 1.3 77.8 - - - +
724B ARG* 1.3 59.5 + - - +
725B LEU 3.1 0.2 - - - -
726B GLY* 3.2 20.6 + - - +
728B LEU* 6.1 0.4 - - - -
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Residues in contact with ARG 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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524B LYS* 4.8 5.3 - - - +
525B LEU* 2.8 34.7 + - - +
526B GLU* 2.9 28.5 + - - +
527B LEU* 4.7 10.0 - - - +
720B LEU 4.3 3.3 + - - +
721B ALA* 3.6 18.3 + - - +
723B GLY* 1.3 75.5 - - - +
725B LEU* 1.3 67.4 + - + +
726B GLY 3.3 0.4 - - - -
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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