Contacts of the helix formed by residues 710 - 714 (chain A) in PDB entry 4I1R
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 PRO 710 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A GLU 4.0 4.9 - - - +
587A PRO* 3.7 28.0 - - + -
612A MET* 4.0 15.7 - - + -
675A LEU* 3.5 11.5 - - + +
678A LEU* 4.2 6.3 - - + -
682A LEU* 4.0 13.9 - - + -
707A VAL* 3.9 18.6 - - + +
708A GLY 3.3 13.2 - - - +
709A LYS* 1.4 79.8 - - - +
711A LEU* 1.4 72.8 + - + +
713A ALA* 2.9 26.1 + - + +
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Residues in contact with LEU 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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582A LYS 4.8 0.5 - - - +
583A ALA 3.0 19.6 - - - +
584A HIS* 4.0 29.4 - - + +
585A GLU 3.1 16.7 + - - +
586A LEU* 3.7 26.7 - - + -
606A ALA* 4.1 13.0 - - + -
608A PHE 3.8 20.4 - - - +
609A SER* 3.3 10.1 - - - +
611A VAL 4.0 4.5 - - - +
612A MET* 3.7 20.4 - - + -
675A LEU* 3.6 19.1 - - + -
709A LYS 3.9 0.2 + - - -
710A PRO* 1.4 74.4 - - + +
712A ILE* 1.3 59.8 + - - +
713A ALA 3.1 5.5 + - - -
714A LYS* 3.2 17.5 + - - +
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Residues in contact with ILE 712 (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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381A VAL* 4.7 9.0 - - + -
383A LEU* 3.8 23.1 - - + -
583A ALA* 3.3 11.2 + - + +
584A HIS* 5.7 0.4 - - - +
609A SER* 3.1 28.4 + - - +
610A ASN* 3.8 21.1 - - + -
675A LEU* 4.3 1.1 - - + -
676A GLN* 4.0 18.3 - - + +
711A LEU* 1.3 76.5 - - - +
713A ALA* 1.3 54.5 + - - +
714A LYS 3.1 1.6 + - - -
715A LEU* 2.8 52.0 + - + +
717A MET* 3.9 26.7 - - - -
801A LZU 4.5 7.0 - - + -
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Residues in contact with ALA 713 (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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675A LEU* 3.3 29.2 - - + +
676A GLN* 5.2 1.3 - - - +
678A LEU* 3.7 33.5 - - + +
709A LYS* 3.6 16.1 - - - +
710A PRO* 2.9 23.6 + - + +
712A ILE* 1.3 78.6 - - - +
714A LYS* 1.3 65.1 + - - +
715A LEU 3.4 5.6 - - - +
716A ASP* 4.2 1.6 + - - -
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Residues in contact with LYS 714 (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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582A LYS* 3.2 67.1 + - + +
583A ALA* 5.2 2.5 - - - -
585A GLU* 5.6 5.7 - - + +
709A LYS* 3.5 38.7 + - + +
711A LEU 3.2 15.4 + - - +
712A ILE 3.1 0.6 - - - -
713A ALA* 1.3 79.3 - - - +
715A LEU* 1.3 62.7 + - + +
716A ASP 3.4 2.9 + - - -
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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