Contacts of the helix formed by residues 713 - 724 (chain I) in PDB entry 6G52
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 ARG 713 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610I ASP* 4.2 19.4 + - + -
611I TYR* 5.6 0.4 - - - +
643I ALA 4.1 7.4 - - - +
644I LEU* 3.6 37.2 - - - +
645I THR 5.5 0.4 - - - +
712I THR* 1.3 73.8 - - - +
714I GLN* 1.3 57.6 + - - +
716I TYR* 3.3 2.5 + - - +
717I GLN* 2.9 30.5 + - - +
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Residues in contact with GLN 714 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712I THR* 3.3 6.1 - - - -
713I ARG* 1.3 79.6 - - - +
715I GLN* 1.3 58.2 + - + +
717I GLN* 3.4 5.6 + - - +
718I ASN* 2.9 31.2 + - - +
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Residues in contact with GLN 715 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578I LEU* 4.0 25.9 - - + +
581I TYR* 4.9 5.5 - - - +
582I PRO 4.2 16.6 + - - -
583I ASP* 5.6 1.6 - - - +
584I VAL* 4.1 13.2 - - - +
710I LYS 3.7 7.1 - - - +
711I ILE* 3.6 10.6 - - - -
712I THR* 3.1 35.6 + - - +
714I GLN* 1.3 77.2 - - + +
716I TYR* 1.3 57.2 + - - +
718I ASN* 3.4 6.0 + - - +
719I GLY* 2.9 26.3 + - - -
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Residues in contact with TYR 716 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565I PHE* 6.0 5.4 - - + -
578I LEU* 5.9 2.7 - - - -
644I LEU* 3.9 25.4 - - + +
711I ILE* 5.4 7.6 - - + +
712I THR 2.8 20.5 + - - +
713I ARG 3.6 4.5 - - - +
714I GLN 3.2 0.2 - - - -
715I GLN* 1.3 74.0 - - - +
717I GLN* 1.3 57.7 + - - +
719I GLY* 3.3 2.0 + - - -
720I LEU* 2.9 29.3 + - - +
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Residues in contact with GLN 717 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644I LEU 5.9 0.9 - - - +
713I ARG 2.9 17.3 + - - +
714I GLN* 3.9 5.2 - - - +
716I TYR* 1.3 75.7 - - - +
718I ASN* 1.3 59.5 + - - +
720I LEU* 3.3 7.3 + - - +
721I LEU* 2.9 30.5 + - - +
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Residues in contact with ASN 718 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714I GLN 2.9 18.3 + - - +
715I GLN* 3.7 7.4 - - - +
717I GLN* 1.3 77.6 - - - +
719I GLY* 1.3 56.0 + - - +
721I LEU* 3.4 5.8 + - - +
722I ALA* 2.9 30.7 + - - +
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Residues in contact with GLY 719 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570I ILE* 4.5 8.8 - - - +
574I ILE* 3.9 24.6 - - - +
578I LEU* 5.3 8.7 - - - +
715I GLN 2.9 14.8 + - - -
716I TYR 3.7 2.5 - - - -
718I ASN* 1.3 73.0 - - - +
720I LEU* 1.3 59.9 + - - +
722I ALA* 3.8 2.3 - - - +
723I SER* 2.9 29.5 + - - -
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Residues in contact with LEU 720 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569I LEU* 3.6 24.6 - - + +
570I ILE* 4.7 2.5 - - + +
716I TYR 2.9 17.1 + - - +
717I GLN* 3.6 8.1 - - - +
719I GLY* 1.3 75.8 - - - +
721I LEU* 1.3 61.6 + - - +
723I SER* 3.2 4.3 + - - -
724I ARG* 3.2 19.6 + - - +
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Residues in contact with LEU 721 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717I GLN 2.9 17.4 + - - +
718I ASN* 3.8 6.7 - - - +
720I LEU* 1.3 75.0 - - - +
722I ALA* 1.3 62.4 + - - +
724I ARG* 3.1 21.5 + - - +
725I MSE 3.6 5.9 + - - +
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Residues in contact with ALA 722 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574I ILE* 3.3 24.2 - - + +
718I ASN 2.9 18.3 + - - +
719I GLY* 3.9 4.3 - - - +
721I LEU* 1.3 76.7 - - - +
723I SER* 1.3 62.3 + - - +
725I MSE 3.3 21.9 - - - +
726I GLU 4.6 0.3 + - - -
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Residues in contact with SER 723 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568I SER 5.3 2.7 - - - -
569I LEU 3.9 11.4 - - - -
571I SER* 3.3 37.9 - - - -
574I ILE* 3.3 8.0 - - - +
719I GLY 2.9 17.2 + - - -
720I LEU 3.5 5.8 - - - -
721I LEU 3.2 0.6 - - - -
722I ALA* 1.3 77.2 - - - +
724I ARG* 1.3 60.5 + - - +
725I MSE 3.1 3.4 + - - -
726I GLU 3.4 17.2 + - - +
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Residues in contact with ARG 724 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720I LEU 3.2 10.7 + - - +
721I LEU* 3.1 15.8 + - - +
723I SER* 1.3 74.3 - - - +
725I MSE 1.3 64.3 + - - +
726I GLU 3.2 7.6 + - - +
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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