Contacts of the helix formed by residues 697 - 710 (chain A) in PDB entry 6T8B
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 697 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ASP* 4.0 20.0 - - - -
422A ARG* 4.5 4.7 - - - +
695A PHE* 3.6 26.9 - - - -
696A VAL* 1.3 77.2 - - - +
698A ASP* 1.3 66.8 + - - +
699A ASP* 3.6 17.1 + - - +
700A GLU* 3.0 25.0 + - - +
701A VAL 3.5 2.8 + - - -
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Residues in contact with ASP 698 (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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506A ILE* 3.2 30.7 - - - +
696A VAL 3.6 2.7 + - - -
697A SER* 1.3 75.7 + - - +
699A ASP* 1.3 64.2 + - - +
701A VAL* 3.0 12.8 + - - +
702A HIS* 2.9 38.9 + - + -
548F ARG* 3.8 38.3 - - - +
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Residues in contact with ASP 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 5.2 1.6 - - - +
697A SER* 3.2 12.3 + - - +
698A ASP* 1.3 79.7 - - - +
700A GLU* 1.3 56.3 - - - +
702A HIS* 3.3 14.9 + - - +
703A ARG* 2.9 52.2 + - - +
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Residues in contact with GLU 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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320A LEU 5.0 0.4 - - - -
321A LEU* 3.6 25.7 - - + +
322A ASP* 3.0 57.7 + - - +
422A ARG* 3.3 9.2 + - - -
423A PHE* 4.2 7.2 + - - +
481A LEU* 4.7 1.1 - - + -
695A PHE 5.0 0.2 - - - +
696A VAL* 3.3 29.5 - - + +
697A SER 3.0 18.1 + - - +
699A ASP* 1.3 77.8 - - - +
701A VAL* 1.3 56.3 + - - +
703A ARG* 3.2 13.1 + - - +
704A VAL* 3.0 34.8 + - - +
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Residues in contact with VAL 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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477A ASN* 4.3 16.6 - - + +
481A LEU* 3.8 18.6 - - + -
506A ILE* 3.6 22.4 - - + -
507A TYR* 3.4 32.3 - - + -
696A VAL* 3.7 26.0 - - + +
697A SER 4.1 3.8 - - - +
698A ASP* 3.0 17.1 + - - +
700A GLU* 1.3 76.1 - - - +
702A HIS* 1.3 58.3 + - - +
704A VAL* 3.3 2.6 + - - +
705A VAL* 2.9 34.0 + - - +
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Residues in contact with HIS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE* 3.6 28.7 - - + +
698A ASP* 2.9 53.9 + - - -
699A ASP* 3.6 17.5 - - - +
701A VAL* 1.3 74.5 - - - +
703A ARG* 1.3 64.4 + - - +
705A VAL* 3.3 4.6 + - - +
706A GLU* 2.9 32.9 + - + +
546F GLY* 6.5 1.6 - - - -
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Residues in contact with ARG 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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320A LEU* 3.2 39.8 + - + +
322A ASP* 3.0 32.5 + - - -
699A ASP* 2.9 29.6 + - - +
700A GLU* 3.2 34.8 + - - +
702A HIS* 1.3 77.2 - - + +
704A VAL* 1.3 58.2 + - - +
706A GLU* 3.3 5.0 + - - +
707A ALA* 2.9 29.2 + - - +
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Residues in contact with VAL 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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316A PRO* 5.4 0.7 - - + -
320A LEU* 4.8 6.3 - - + +
321A LEU* 5.1 2.5 - - + -
481A LEU* 3.8 19.3 - - + -
484A LEU* 4.1 18.6 - - + -
485A PHE* 3.4 41.5 - - + -
507A TYR* 6.5 0.2 - - + -
700A GLU 3.0 16.9 + - - +
701A VAL* 3.8 4.7 - - - +
702A HIS 3.2 0.4 - - - -
703A ARG* 1.3 75.0 - - + +
705A VAL* 1.3 67.2 + - + +
707A ALA* 3.2 6.7 + - - +
708A TRP* 2.9 48.6 + - + +
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Residues in contact with VAL 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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484A LEU* 5.6 1.6 - - + -
506A ILE* 3.2 32.8 - - + +
507A TYR* 3.6 27.6 - - + -
508A GLU 4.5 4.5 - - - +
510A ILE* 3.9 19.2 - - + +
701A VAL 2.9 21.9 + - - +
702A HIS* 3.9 5.8 - - - +
704A VAL* 1.3 76.8 - - + +
706A GLU* 1.3 61.2 + - + +
708A TRP* 3.3 2.4 + - - +
709A LYS* 2.9 46.3 + - + +
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Residues in contact with GLU 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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702A HIS* 2.9 25.4 + - + +
703A ARG* 3.8 4.7 - - - +
705A VAL* 1.3 80.3 - - + +
707A ALA* 1.3 57.1 + - - +
709A LYS* 3.2 26.6 + - - +
710A LEU* 2.9 45.7 + - + +
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Residues in contact with ALA 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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316A PRO* 4.4 3.6 - - + -
320A LEU* 3.8 25.4 - - + -
703A ARG 2.9 18.3 + - - +
704A VAL* 3.2 5.4 + - - +
706A GLU* 1.3 76.4 - - - +
708A TRP* 1.3 59.5 + - - +
710A LEU* 3.8 12.5 + - - +
711A ARG* 2.5 46.2 + - - +
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Residues in contact with TRP 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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314A THR 5.6 0.7 - - - -
315A LEU* 3.9 16.8 - - + -
316A PRO* 3.5 30.8 - - + +
484A LEU* 3.0 45.5 + - + +
487A SER 3.8 7.9 - - - -
488A THR* 4.3 5.4 - - + -
489A PRO* 3.9 13.7 - - + -
510A ILE* 4.0 10.1 - - + -
511A PRO* 3.8 31.1 - - + +
512A HIS* 3.5 31.2 - + - -
704A VAL* 2.9 39.7 + - + +
705A VAL 3.8 3.6 - - - +
707A ALA* 1.3 74.5 - - - +
709A LYS* 1.3 59.7 + - - +
710A LEU 3.0 1.1 - - - -
711A ARG* 2.8 34.8 + - + +
712A GLY 3.3 8.7 + - - -
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Residues in contact with LYS 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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508A GLU 4.0 16.8 + - - +
509A GLY* 3.9 27.1 - - - +
510A ILE 4.2 2.2 - - - +
705A VAL* 2.9 39.3 + - + +
706A GLU* 3.2 25.9 + - - +
708A TRP* 1.3 75.6 - - - +
710A LEU* 1.3 60.3 + - + +
711A ARG 3.2 0.2 - - - -
712A GLY 3.4 19.4 - - - +
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Residues in contact with LEU 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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706A GLU* 2.9 30.9 + - + +
707A ALA* 4.0 10.1 - - - +
708A TRP 3.0 0.6 - - - -
709A LYS* 1.3 79.2 - - + +
711A ARG* 1.3 62.6 + - + +
712A GLY 3.7 0.9 - - - -
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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