Contacts of the helix formed by residues 715 - 726 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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679D GLU* 3.7 31.9 - - - -
683D GLU* 2.9 27.4 + - - -
713D ALA 3.3 3.7 + - - -
714D THR* 1.3 75.8 - - - +
716D ARG* 1.3 63.2 - - - +
717D PRO* 3.3 12.8 - - - +
718D SER* 3.0 17.3 + - - -
719D LYS* 2.9 20.9 + - - +
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Residues in contact with ARG 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C PRO 5.6 0.4 + - - -
581C LYS* 3.5 22.2 + - - +
583C GLU* 3.0 45.1 + - + +
679D GLU* 5.5 1.0 + - - -
714D THR 3.9 0.6 + - - -
715D SER* 1.3 71.2 - - - +
717D PRO* 1.3 72.6 - - + +
719D LYS* 3.1 9.4 + - - -
720D LEU* 2.9 60.9 + - + +
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Residues in contact with PRO 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D ARG* 4.5 22.0 - - + -
679D GLU* 4.5 5.2 - - - +
715D SER* 3.3 15.0 - - - +
716D ARG* 1.3 96.5 - - + +
718D SER* 1.3 55.3 + - - +
720D LEU* 3.6 9.3 + - + +
721D ALA* 3.0 28.1 + - - +
740D ARG* 6.3 0.4 - - - +
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Residues in contact with SER 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D GLU* 2.6 29.0 + - - -
714D THR* 3.6 12.1 - - - -
715D SER* 3.0 11.1 + - - -
717D PRO* 1.3 77.3 - - - +
719D LYS* 1.3 59.5 + - - +
721D ALA* 3.1 4.8 + - - +
722D LEU* 2.9 33.4 + - - +
733D PHE* 4.6 0.9 - - - -
736D LEU* 3.6 16.8 - - - +
740D ARG* 2.7 25.8 + - - +
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Residues in contact with LYS 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C PRO 3.5 21.8 + - - +
579C HIS 2.7 28.8 + - - -
580C PRO* 4.8 6.3 + - - +
582C LYS 3.2 10.5 + - - +
583C GLU* 3.0 37.4 + - + +
711D LEU 5.8 0.2 - - - +
714D THR* 3.4 34.5 - - + +
715D SER 2.9 10.5 + - - +
716D ARG* 3.1 8.5 + - - +
718D SER* 1.3 77.1 - - - +
720D LEU* 1.3 57.9 + - + +
722D LEU* 3.1 7.5 + - - +
723D GLY* 2.7 33.6 + - - -
728D LEU* 4.2 21.8 - - + +
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Residues in contact with LEU 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C PRO 4.7 12.3 - - - +
583C GLU* 5.4 1.3 - - - +
716D ARG* 2.9 63.5 + - + +
717D PRO* 3.9 7.4 - - + +
719D LYS* 1.3 82.8 - - + +
721D ALA* 1.3 62.3 + - - +
723D GLY* 3.3 2.4 + - - +
724D ARG* 2.9 47.4 + - - +
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Residues in contact with ALA 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717D PRO 3.0 15.8 + - - +
718D SER* 3.1 12.3 + - - +
720D LEU* 1.3 79.1 - - - +
722D LEU* 1.3 61.6 + - - +
724D ARG* 3.6 12.3 + - - +
725D LEU* 3.4 16.1 + - - +
736D LEU* 4.7 16.6 - - + -
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Residues in contact with LEU 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D LEU* 4.3 4.9 - - + -
714D THR* 4.9 6.1 - - + -
718D SER 2.9 21.4 + - - +
719D LYS* 3.7 3.6 - - - +
721D ALA* 1.3 75.3 - - - +
723D GLY* 1.3 66.7 + - - +
725D LEU* 3.2 23.4 - - + +
726D GLY 3.0 17.3 + - - -
727D VAL 3.3 19.1 + - - +
728D LEU* 4.7 13.0 - - + -
729D SER 4.9 0.7 - - - +
732D SER* 3.7 26.0 - - - +
733D PHE* 3.7 35.7 - - + +
736D LEU* 3.9 24.5 - - + -
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Residues in contact with GLY 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719D LYS 2.7 20.3 + - - -
720D LEU* 3.3 3.8 + - - -
721D ALA 3.3 0.6 - - - -
722D LEU* 1.3 72.4 - - - +
724D ARG* 1.3 62.6 + - - +
726D GLY* 2.9 17.3 + - - -
727D VAL 5.4 0.2 - - - -
728D LEU* 5.6 6.3 - - - +
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Residues in contact with ARG 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720D LEU* 2.9 46.2 + - - +
721D ALA* 3.6 12.7 - - - +
722D LEU 3.3 0.2 - - - -
723D GLY* 1.3 75.3 - - - +
725D LEU* 1.3 65.6 + - - +
726D GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D VAL* 4.3 15.9 - - + -
525D LEU* 3.9 40.4 - - + +
526D GLU* 6.0 0.7 - - - +
527D LEU* 3.0 43.8 - - + +
721D ALA 3.4 5.1 + - - +
722D LEU* 3.2 33.6 + - + +
723D GLY 3.1 0.2 - - - -
724D ARG* 1.3 81.9 - - - +
726D GLY* 1.3 55.2 + - - +
727D VAL* 3.0 37.9 - - + +
732D SER* 4.4 8.5 - - - -
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Residues in contact with GLY 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D LEU* 4.6 4.7 - - - -
722D LEU 3.0 2.3 + - - -
723D GLY* 2.9 16.0 + - - -
724D ARG 4.1 1.3 - - - -
725D LEU* 1.3 78.2 - - - +
727D VAL* 1.3 68.2 + - - +
728D LEU 4.4 0.2 - - - -
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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