Contacts of the helix formed by residues 677 - 687 (chain A) in PDB entry 6T2C
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 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A GLU* 5.6 1.1 - - - -
675A THR* 4.4 2.2 - - - -
676A PHE* 1.3 81.0 - - - +
678A LEU* 1.3 62.0 + - - +
679A LYS* 3.9 14.6 + - - +
680A GLY* 3.9 13.4 + - - -
681A LEU* 3.6 12.6 + - - +
479B GLN* 3.3 27.9 + - + +
480B LYS* 3.9 31.7 - - - +
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Residues in contact with LEU 678 (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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258A GLU* 5.1 10.6 + - - +
260A PHE* 4.1 30.1 - - + -
265A ILE* 4.4 9.6 - - + -
660A LEU* 5.2 3.4 - - + -
663A LEU* 4.6 2.7 - - + -
675A THR* 3.6 34.6 + - + +
676A PHE 4.2 0.6 - - - -
677A ASP* 1.3 73.4 + - - +
679A LYS* 1.3 63.2 + - + +
680A GLY 3.3 0.4 - - - -
681A LEU* 3.2 20.8 + - + +
682A TYR* 3.0 50.5 + - + -
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Residues in contact with LYS 679 (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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258A GLU* 5.3 12.5 + - - +
677A ASP* 3.4 11.9 - - - +
678A LEU* 1.3 81.3 - - + +
680A GLY* 1.3 57.7 + - - +
682A TYR* 3.4 9.3 + - - +
683A GLU* 2.9 40.6 + - + +
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Residues in contact with GLY 680 (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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677A ASP* 3.7 11.4 + - - -
678A LEU 3.3 0.6 - - - -
679A LYS* 1.3 79.9 - - - +
681A LEU* 1.3 56.0 + - - +
683A GLU* 3.4 9.0 + - - +
684A ALA* 2.9 30.1 + - - +
480B LYS* 4.0 38.3 + - - +
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Residues in contact with LEU 681 (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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656A GLU* 3.5 37.9 - - - +
659A LYS* 4.3 25.6 - - + -
660A LEU* 3.7 26.2 - - + -
663A LEU* 4.4 9.4 - - + -
675A THR* 5.3 3.4 - - + -
677A ASP 3.6 7.6 + - - +
678A LEU* 3.2 24.7 + - + +
680A GLY* 1.3 73.6 - - - +
682A TYR* 1.3 65.4 + - - +
684A ALA* 3.3 2.7 + - - +
685A ILE* 3.0 28.9 + - - +
480B LYS* 3.9 24.7 - - - +
481B LYS* 5.1 0.7 - - + -
482B SER 6.2 0.2 - - - +
483B TYR* 6.1 0.9 - - + -
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Residues in contact with TYR 682 (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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265A ILE* 3.5 26.6 - - + +
266A ARG* 2.7 69.7 + - + +
267A GLU 4.7 0.2 - - - -
268A LEU* 3.6 31.0 - - + -
660A LEU* 4.1 20.6 - - + +
678A LEU* 3.0 47.2 + - + +
679A LYS* 3.6 11.4 - - - +
680A GLY 3.3 0.2 - - - -
681A LEU* 1.3 77.2 - - - +
683A GLU* 1.3 57.7 + - + +
685A ILE* 3.4 6.3 + - + +
686A GLU* 2.9 35.9 + - - +
702A PHE* 6.0 0.2 - + - -
706A LEU* 4.6 1.0 - - - +
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Residues in contact with GLU 683 (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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266A ARG* 5.9 0.9 - - - +
679A LYS* 2.9 26.2 + - + +
680A GLY* 3.9 8.8 - - - +
682A TYR* 1.3 78.0 - - + +
684A ALA* 1.3 57.2 + - - +
686A GLU* 4.2 10.0 - - - +
687A GLU* 3.0 33.1 + - - +
480B LYS* 5.3 5.5 + - - +
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Residues in contact with ALA 684 (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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656A GLU* 3.9 28.2 - - + +
680A GLY 2.9 18.1 + - - +
681A LEU* 3.8 6.7 - - + +
683A GLU* 1.3 72.7 - - - +
685A ILE* 1.3 65.7 + - - +
687A GLU* 3.5 13.7 - - - +
688A CYS* 3.5 20.1 - - - -
480B LYS* 5.8 3.6 - - + -
481B LYS* 4.7 11.0 - - + +
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Residues in contact with ILE 685 (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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268A LEU* 4.0 25.4 - - + -
652A GLY 5.4 0.4 - - - -
653A PHE* 3.7 34.2 - - + +
656A GLU* 3.3 38.4 - - + +
657A SER* 3.8 11.4 - - - -
660A LEU* 3.7 28.3 - - + -
681A LEU 3.0 14.4 + - - +
682A TYR* 3.7 7.0 - - - +
684A ALA* 1.3 78.0 - - - +
686A GLU* 1.3 59.6 + - - +
688A CYS* 3.0 28.9 + - - +
689A ILE* 4.2 4.7 - - + +
702A PHE* 5.8 0.2 - - + -
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Residues in contact with GLU 686 (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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266A ARG* 3.0 36.8 + - - -
268A LEU* 3.8 18.2 - - + -
269A GLU* 3.0 44.6 + - - +
682A TYR 2.9 20.2 + - - +
683A GLU* 3.3 9.9 + - - +
685A ILE* 1.3 75.7 - - - +
687A GLU* 1.3 60.5 - - - +
688A CYS 3.2 0.8 + - - -
689A ILE* 3.7 24.9 + - + +
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Residues in contact with GLU 687 (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 GLU 3.0 15.4 + - - +
684A ALA* 3.5 21.2 - - - +
686A GLU* 1.3 78.1 - - - +
688A CYS* 1.3 68.9 + - - +
689A ILE 3.3 4.6 + - - -
690A ILE* 3.9 14.8 - - - +
236B LEU* 3.8 21.4 - - + +
237B LYS* 4.7 16.8 + - - +
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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