Contacts of the helix formed by residues 682 - 693 (chain A) in PDB entry 6QNW
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 682 (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* 3.4 1.6 - - - -
680A THR* 4.7 1.3 - - - -
681A PHE* 1.3 75.6 - - - +
683A LEU* 1.3 61.5 + - - +
684A GLU* 3.2 13.9 + - - +
685A GLY* 2.8 35.1 + - - -
686A LEU* 3.3 10.6 + - - +
479B LYS* 3.0 36.8 + - + +
480B LYS* 3.9 12.6 - - + +
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Residues in contact with LEU 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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258A GLU* 2.9 16.4 + - - +
260A PHE* 4.6 13.2 - - + -
264A THR* 4.2 33.0 - - + +
265A PRO* 5.2 0.9 - - + -
665A LEU* 4.5 13.9 - - + -
680A THR* 3.9 25.6 + - + +
682A ASP* 1.3 69.2 - - - +
684A GLU* 1.3 61.4 + - + +
686A LEU* 3.2 26.1 + - + +
687A TYR* 2.9 46.9 + - + +
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Residues in contact with GLU 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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682A ASP* 3.2 9.5 + - - +
683A LEU* 1.3 79.9 - - + +
685A GLY* 1.3 56.1 + - - +
687A TYR* 3.3 17.8 + - - +
688A GLU* 2.8 46.5 + - + +
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Residues in contact with GLY 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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682A ASP* 2.8 26.7 + - - -
683A LEU 3.2 0.4 - - - -
684A GLU* 1.3 73.7 - - - +
686A LEU* 1.3 58.9 + - - +
688A GLU* 3.3 8.9 + - - +
689A ALA* 2.9 28.9 + - - +
480B LYS* 3.7 25.6 - - - +
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Residues in contact with LEU 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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661A GLU* 3.5 40.2 - - + +
664A LYS* 4.5 13.2 - - + -
665A LEU* 3.9 34.5 - - + +
668A VAL* 6.2 1.3 - - + -
682A ASP 3.3 9.7 + - - +
683A LEU* 3.2 27.4 + - + +
685A GLY* 1.3 75.7 - - - +
687A TYR* 1.3 59.4 + - + +
689A ALA* 3.2 5.6 + - - +
690A ILE* 2.9 38.2 + - + +
480B LYS* 4.3 21.1 - - - +
481B LYS* 5.6 0.4 - - + -
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Residues in contact with TYR 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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264A THR 5.3 0.4 - - - -
265A PRO* 3.8 8.0 - - - +
266A ARG* 2.4 54.4 + - + -
267A PRO 4.9 4.3 - - - -
268A ILE* 5.2 6.1 - - + -
269A ARG* 6.3 3.1 - - + -
665A LEU* 3.9 30.2 - - + +
683A LEU* 2.9 40.4 + - + +
684A GLU* 3.7 19.5 - - - +
685A GLY 3.3 0.2 - - - -
686A LEU* 1.3 80.1 - - + +
688A GLU* 1.3 59.3 + - + +
690A ILE* 3.2 12.4 + - + +
691A GLU* 2.9 50.1 + - + +
711A LEU* 4.8 1.9 - - - +
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Residues in contact with GLU 688 (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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269A ARG* 5.1 10.8 + - - -
684A GLU* 2.8 39.2 + - + +
685A GLY* 3.3 8.3 + - - +
687A TYR* 1.3 77.3 - - - +
689A ALA* 1.3 57.6 + - - +
691A GLU* 3.3 9.2 + - - +
692A GLU* 2.9 32.0 + - - +
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Residues in contact with ALA 689 (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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661A GLU* 3.7 32.8 - - + +
685A GLY 2.9 14.2 + - - +
686A LEU* 3.6 9.2 - - - +
688A GLU* 1.3 75.5 - - - +
690A ILE* 1.3 63.8 + - - +
692A GLU* 3.4 23.2 + - - +
693A CYS* 3.7 11.1 + - - +
480B LYS* 6.0 3.1 - - + -
481B LYS* 6.1 1.6 - - + -
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Residues in contact with ILE 690 (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 ILE* 3.7 35.2 - - + -
658A PHE* 3.9 17.7 - - + -
661A GLU* 3.7 31.4 - - + +
662A SER* 4.3 12.3 - - - +
665A LEU* 4.3 21.3 - - + -
686A LEU* 2.9 26.6 + - + +
687A TYR* 3.7 12.8 - - + +
688A GLU 3.2 0.2 - - - -
689A ALA* 1.3 77.3 - - - +
691A GLU* 1.3 63.5 + - - +
692A GLU 3.2 0.5 + - - -
693A CYS* 3.3 21.7 - - - -
694A LEU* 3.3 10.5 - - + +
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Residues in contact with GLU 691 (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 ILE* 3.5 15.3 - - - +
269A ARG* 2.8 75.4 + - + +
687A TYR* 2.9 39.7 + - + +
688A GLU* 3.9 10.5 - - - +
690A ILE* 1.3 76.5 - - - +
692A GLU* 1.3 62.2 + - - +
694A LEU* 3.6 22.6 + - - +
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Residues in contact with GLU 692 (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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688A GLU 2.9 15.8 + - - +
689A ALA* 3.6 16.4 - - - +
690A ILE 3.1 1.0 - - - -
691A GLU* 1.3 78.9 - - - +
693A CYS* 1.3 56.6 + - + +
694A LEU 3.4 2.8 + - - -
695A ILE* 3.8 14.2 - - - +
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Residues in contact with CYS 693 (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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654A GLN* 3.6 33.0 - - - +
657A GLY* 3.8 9.2 - - - -
658A PHE* 3.5 35.4 - - - +
661A GLU* 5.2 0.9 - - - -
689A ALA 3.7 10.5 - - - +
690A ILE* 3.3 17.0 - - - -
691A GLU 3.3 0.2 - - - -
692A GLU* 1.3 77.2 - - + +
694A LEU* 1.3 63.7 + - - +
695A ILE* 4.0 10.1 - - - -
700A VAL* 3.6 5.4 - - - +
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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