Contacts of the helix formed by residues 715 - 726 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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679C GLU* 3.8 33.1 + - - +
680C GLN* 6.2 0.2 - - - +
683C GLU* 2.7 27.9 + - - -
713C ALA 3.4 3.4 + - - -
714C THR* 1.3 76.1 - - - +
716C ARG* 1.3 64.7 + - - +
717C PRO* 3.4 11.9 - - - +
718C SER* 3.0 17.5 + - - -
719C LYS* 3.0 21.0 + - - +
583D GLU* 5.5 1.6 - - - -
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Residues in contact with ARG 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679C GLU* 5.1 8.5 + - - -
714C THR 3.9 0.4 + - - -
715C SER* 1.3 70.9 - - - +
717C PRO* 1.3 74.3 - - + +
719C LYS* 3.2 11.3 + - + +
720C LEU* 3.0 34.7 + - + +
581D LYS 5.9 3.1 - - - -
583D GLU* 2.8 51.1 + - + +
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Residues in contact with PRO 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ARG* 6.3 3.8 - - + -
679C GLU* 4.1 15.0 - - - +
715C SER* 3.4 14.6 - - - +
716C ARG* 1.3 95.4 - - + +
718C SER* 1.3 55.0 + - - +
720C LEU* 3.6 8.8 + - + +
721C ALA* 3.1 28.1 + - - +
724C ARG* 5.0 1.6 + - - -
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Residues in contact with SER 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C GLU* 2.7 30.4 + - - -
714C THR* 3.6 11.9 - - - -
715C SER* 3.0 10.3 + - - -
717C PRO* 1.3 77.6 - - - +
719C LYS* 1.3 64.4 + - - +
721C ALA* 3.3 3.9 + - - +
722C LEU* 3.0 28.6 + - - +
733C PHE* 4.6 0.9 - - - -
736C LEU* 3.7 17.5 - - - -
740C ARG* 2.8 23.7 + - - +
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Residues in contact with LYS 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C LEU 5.7 0.4 - - - +
714C THR* 3.3 37.5 - - + +
715C SER 3.0 11.3 + - - +
716C ARG* 3.2 10.5 + - + +
718C SER* 1.3 76.8 - - - +
720C LEU* 1.3 52.6 + - + +
722C LEU* 3.1 5.7 + - - +
723C GLY* 2.7 33.4 + - - -
728C LEU* 4.3 20.9 - - + +
577D PRO 3.5 19.6 + - - +
578D GLU 4.7 2.2 - - - -
579D HIS 2.7 29.9 + - - -
580D PRO 4.3 11.6 + - - +
581D LYS 4.9 0.6 - - - -
582D LYS 3.1 25.9 + - - +
583D GLU* 4.2 14.6 - - + +
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Residues in contact with LEU 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C ARG* 3.0 27.3 + - + +
717C PRO* 3.9 7.0 - - + +
719C LYS* 1.3 77.5 - - + +
721C ALA* 1.3 62.3 + - - +
723C GLY* 3.2 2.9 + - - +
724C ARG* 3.0 44.6 + - - +
580D PRO 4.6 14.1 - - - +
581D LYS* 6.1 2.0 - - + -
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Residues in contact with ALA 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717C PRO 3.1 18.0 + - - +
718C SER* 3.6 7.9 - - - +
719C LYS 3.2 0.2 - - - -
720C LEU* 1.3 77.0 - - - +
722C LEU* 1.3 59.6 + - - +
724C ARG* 3.3 25.4 + - - +
725C LEU* 3.0 24.8 + - - +
736C LEU* 4.6 16.4 - - + -
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Residues in contact with LEU 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C LEU* 4.4 1.8 - - + -
714C THR* 4.8 5.6 - - + +
718C SER 3.0 22.8 + - - +
719C LYS 3.6 4.0 - - - +
721C ALA* 1.3 74.8 - - - +
723C GLY* 1.3 60.9 + - - +
725C LEU* 3.2 18.5 + - + +
726C GLY 2.8 23.6 + - - -
727C VAL 3.3 17.8 + - - +
728C LEU* 4.3 19.5 - - + -
729C SER 4.8 0.7 - - - +
732C SER* 3.6 36.8 - - - +
733C PHE* 3.8 31.0 - - + +
736C LEU* 4.0 20.9 - - + -
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Residues in contact with GLY 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C LYS 2.7 15.3 + - - -
720C LEU* 3.6 4.0 - - - -
721C ALA 3.2 0.2 - - - -
722C LEU* 1.3 79.4 - - - +
724C ARG* 1.3 59.8 + - - +
726C GLY* 3.1 15.3 + - - -
728C LEU* 5.1 6.9 - - - +
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Residues in contact with ARG 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717C PRO 5.0 1.4 + - - -
720C LEU* 3.0 35.6 + - - +
721C ALA* 3.6 28.9 - - - +
723C GLY* 1.3 73.3 - - - +
725C LEU* 1.3 66.3 + - - +
726C GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C VAL* 4.2 12.6 - - + -
525C LEU* 3.6 51.8 - - + +
526C GLU* 5.0 2.7 - - - +
527C LEU* 3.7 31.2 + - + +
721C ALA 3.0 13.9 + - - +
722C LEU* 3.3 23.3 - - + +
724C ARG* 1.3 78.0 - - - +
726C GLY* 1.3 57.5 + - - +
727C VAL* 3.2 35.7 - - + +
732C SER* 4.4 6.3 - - - -
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Residues in contact with GLY 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C LEU* 5.0 3.8 - - - -
722C LEU 2.8 7.1 + - - -
723C GLY* 3.1 14.4 + - - -
724C ARG 4.3 0.7 - - - -
725C LEU* 1.3 78.6 - - - +
727C VAL* 1.3 64.7 + - - +
728C LEU 4.2 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