Contacts of the helix formed by residues 683 - 688 (chain B) in PDB entry 6CNC
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 ALA 683 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 5.6 6.5 - - + -
467B LEU* 3.7 27.6 - - + +
471B THR* 4.8 18.1 - - + +
513B ASN* 5.9 1.8 - - - +
514B LEU 4.4 4.9 + - - -
515B ALA 5.0 1.1 - - - +
516B LEU* 3.6 15.8 - - + +
682B GLY* 1.3 73.8 - - - +
684B VAL* 1.3 67.6 + - + +
686B GLY* 3.1 10.9 + - - -
687B LEU 4.5 0.2 + - - -
740B THR* 5.7 0.5 - - - -
744B ILE* 4.2 25.9 - - + +
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Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ILE* 3.6 33.0 - - + -
467B LEU* 5.0 0.9 - - + -
468B GLY* 4.8 9.6 - - - -
501B ASP* 4.9 3.8 - - - +
513B ASN* 5.1 8.2 - - - +
682B GLY 3.5 0.2 - - - -
683B ALA* 1.3 77.9 - - + +
685B ALA* 1.3 63.8 + - - +
686B GLY 2.9 1.6 + - - -
687B LEU* 3.0 26.3 + - + +
688B ILE* 4.4 2.1 - - + +
702B GLN* 5.0 2.7 - - + +
703B CYS* 3.6 36.8 - - + +
706B GLY* 5.2 2.0 - - - -
707B LYS* 4.0 31.0 - - - +
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Residues in contact with ALA 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B CYS* 4.2 2.2 - - - -
500B ALA* 3.6 14.6 - - + -
501B ASP* 6.0 0.2 - - - -
681B LEU* 3.6 35.4 - - + +
682B GLY 3.4 10.9 + - - +
683B ALA 3.2 0.6 - - - -
684B VAL* 1.3 77.6 - - - +
686B GLY* 1.3 62.1 + - - +
688B ILE* 3.1 24.7 + - + +
703B CYS* 3.4 27.4 - - - -
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Residues in contact with GLY 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B LEU* 4.9 4.0 - - - +
682B GLY 3.3 7.0 + - - -
683B ALA 3.1 10.9 + - - -
684B VAL 2.9 2.8 + - - -
685B ALA* 1.3 77.1 - - - +
687B LEU* 1.3 62.1 + - - +
688B ILE 3.2 2.0 + - - +
738B THR* 3.1 28.4 - - - +
740B THR* 3.0 27.3 + - - -
741B ILE* 3.6 4.1 - - - +
744B ILE* 5.9 0.9 - - - -
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Residues in contact with LEU 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ILE* 3.7 37.0 - - + -
683B ALA 4.5 0.4 + - - -
684B VAL* 3.0 21.2 + - + +
686B GLY* 1.3 75.5 - - - +
688B ILE* 1.3 64.6 + - + +
689B PRO* 3.1 10.2 - - - +
702B GLN* 5.3 8.1 - - - +
706B GLY* 5.2 9.6 - - - -
738B THR* 4.4 1.0 + - - -
741B ILE* 3.8 14.5 - - + +
744B ILE* 5.1 6.5 - - + +
746B TYR* 3.6 44.9 - - + -
915B ARG* 3.4 25.2 + - + +
1025B GLN* 5.0 9.2 - - - +
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Residues in contact with ILE 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B LEU* 5.4 0.7 - - + -
684B VAL 4.4 2.5 - - - +
685B ALA* 3.1 37.5 + - + +
686B GLY 3.7 3.1 - - - +
687B LEU* 1.3 75.4 - - + +
689B PRO* 1.3 76.8 - - + +
691B PRO* 3.2 30.1 - - + +
694B ASN* 4.3 4.5 - - - +
699B ASN* 3.2 28.0 - - - +
702B GLN* 3.5 36.3 - - + -
703B CYS* 3.8 11.9 - - - -
738B THR* 3.3 10.0 + - - +
915B ARG 3.7 5.4 - - - +
916B HIS* 4.2 12.3 - - - +
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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