Contacts of the helix formed by residues 698 - 711 (chain A) in PDB entry 5I0H
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 ASP 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A PRO* 3.6 18.7 - - - +
697A GLU* 1.3 78.8 + - - +
699A VAL* 1.3 63.7 + - - +
700A ARG* 3.8 10.1 - - + +
701A GLY* 2.8 24.0 + - - -
702A LYS* 3.1 23.2 + - - +
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Residues in contact with VAL 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.7 48.2 - - + +
680A GLN* 3.6 35.4 - - + +
683A TYR* 3.9 17.3 - - + -
697A GLU 3.9 1.2 + - - -
698A ASP* 1.3 69.7 - - - +
700A ARG* 1.4 70.0 + - + +
702A LYS* 3.1 9.2 + - + +
703A CYS* 3.0 22.8 + - - -
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Residues in contact with ARG 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.6 36.1 - - + -
698A ASP* 3.4 9.0 + - + +
699A VAL* 1.4 81.9 - - + +
701A GLY* 1.3 57.7 - - - +
703A CYS* 3.4 4.2 + - - +
704A THR* 2.9 32.8 + - - -
719A LEU* 3.6 39.2 + - + +
720A GLY 2.9 27.3 + - - -
721A LYS* 4.5 4.4 + - - +
379B PHE* 3.6 65.2 - - + +
382B GLY* 6.2 1.0 - - - -
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Residues in contact with GLY 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A PRO* 3.5 21.8 - - - +
698A ASP* 2.8 20.7 + - - -
699A VAL 3.2 0.2 - - - -
700A ARG* 1.3 74.5 - - - +
702A LYS* 1.4 57.5 + - - +
704A THR* 3.4 7.6 + - - -
705A SER* 2.9 32.9 + - - -
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Residues in contact with LYS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A TYR* 3.6 52.7 - - + -
690A MET* 3.8 14.7 - - - +
695A LEU* 4.1 25.1 - - + -
696A PRO* 2.8 35.1 + - - +
697A GLU* 3.0 24.5 + - - +
698A ASP 3.1 10.5 + - - +
699A VAL* 3.1 14.1 + - + +
701A GLY* 1.4 71.4 - - - +
703A CYS* 1.3 65.7 + - - +
705A SER* 3.4 4.0 + - - -
706A LEU 3.3 15.9 + - - -
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Residues in contact with CYS 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.4 31.9 - - - -
682A PHE* 3.6 25.1 - - + -
683A TYR* 4.3 4.5 - - - -
690A MET* 4.7 0.9 - - - -
699A VAL* 3.0 20.7 + - - -
700A ARG* 3.6 8.1 - - - +
702A LYS* 1.3 76.6 - - - +
704A THR* 1.3 62.7 + - - +
706A LEU* 3.3 4.7 + - - +
707A LEU* 3.0 28.7 + - + +
719A LEU* 4.5 4.9 - - + -
724A VAL* 3.7 26.0 - - + -
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Residues in contact with THR 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A ARG 2.9 18.6 + - - -
701A GLY* 3.6 8.9 - - - -
703A CYS* 1.3 75.9 - - - +
705A SER* 1.3 56.5 + - - +
707A LEU* 3.3 7.2 + - - +
708A GLN* 2.8 61.4 + - - +
717A TRP* 3.9 15.5 - - + -
719A LEU* 3.3 20.3 - - - +
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Residues in contact with SER 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A LEU* 3.7 20.6 - - - +
694A ALA 4.6 4.3 + - - -
695A LEU* 3.9 9.2 - - - -
696A PRO* 3.6 14.6 - - - +
701A GLY 2.9 18.1 + - - -
702A LYS 3.7 5.8 - - - -
703A CYS 3.3 0.2 - - - -
704A THR* 1.3 75.2 - - - +
706A LEU* 1.4 62.4 + - - +
708A GLN* 3.9 10.4 - - - +
709A LEU* 3.2 22.5 + - - +
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Residues in contact with LEU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A PHE* 3.9 11.9 - - + -
686A TYR* 3.5 32.1 - - + +
689A LEU* 3.5 30.1 - - + +
690A MET* 3.7 32.8 - - + -
693A LEU* 3.8 6.0 - - + +
702A LYS 3.3 2.2 + - - -
703A CYS 3.3 6.7 + - - +
705A SER* 1.4 77.8 - - - +
707A LEU* 1.3 63.7 + - - +
709A LEU* 3.2 9.3 + - + +
710A TYR* 3.1 44.4 + - + +
734A LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A PHE* 3.7 25.8 - - + -
703A CYS* 3.0 27.3 + - + +
704A THR 3.3 2.7 + - - +
706A LEU* 1.3 76.1 - - - +
708A GLN* 1.3 53.9 + - - +
710A TYR* 3.4 3.5 + - - +
711A ASP* 2.8 36.4 + - - +
717A TRP* 3.6 46.4 + - + -
719A LEU* 4.3 5.6 - - + -
724A VAL* 3.6 26.2 - - + -
726A LEU* 4.6 4.7 - - + -
730A LEU* 3.7 26.8 - - + +
734A LEU* 4.6 4.3 - - + -
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Residues in contact with GLN 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A THR* 2.8 40.5 + - - +
705A SER* 3.9 8.3 + - - +
707A LEU* 1.3 75.1 - - - +
709A LEU* 1.4 61.3 + - - +
711A ASP 4.0 5.4 - - - -
712A ALA* 3.2 29.5 + - + +
714A ASN* 3.8 29.0 - - - +
717A TRP* 3.8 6.5 - - + -
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Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A LEU 4.4 2.9 - - - +
693A LEU* 3.6 32.3 - - + -
705A SER 3.2 14.0 + - - +
706A LEU* 3.5 12.6 - - + +
708A GLN* 1.4 78.1 - - - +
710A TYR* 1.3 82.7 + - + +
712A ALA* 5.0 1.4 + - - +
733A LYS* 5.4 0.2 + - - -
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Residues in contact with TYR 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A LEU* 3.7 11.8 + - + +
706A LEU* 3.1 44.2 + - + +
707A LEU* 4.2 2.5 - - - +
709A LEU* 1.3 93.5 - - + +
711A ASP* 1.3 60.7 + - - +
712A ALA 4.2 0.2 - - - -
716A GLU* 4.9 1.0 - - - +
730A LEU* 3.8 19.2 - - + +
733A LYS* 2.9 58.5 + - + +
734A LEU* 3.8 23.6 - - + -
737A ARG* 3.2 56.3 + - + +
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Residues in contact with ASP 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A LEU 2.8 11.2 + - - +
708A GLN* 3.5 4.1 - - - +
710A TYR* 1.3 78.7 - - - +
712A ALA* 1.3 61.9 + - - +
713A SER* 2.7 24.5 + - - -
714A ASN* 3.2 7.3 + - - +
715A SER 3.3 5.2 + - - -
716A GLU* 2.8 57.3 + - - +
717A TRP* 3.3 23.3 + - + -
730A LEU* 4.2 6.1 - - + -
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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