Contacts of the helix formed by residues 651 - 657 (chain B) in PDB entry 6CNB
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 VAL 651 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A PHE* 4.0 11.2 - - + -
371B TYR* 5.5 3.8 - - + -
372B VAL* 4.2 22.7 - - + +
373B GLY* 3.4 36.1 - - - +
492B SER* 4.3 15.0 - - - +
496B MET* 3.4 29.5 - - + -
607B ARG* 5.4 0.7 - - + -
608B ILE* 5.2 2.0 - - + +
650B ASP* 1.3 89.0 + - - +
652B ASN* 1.3 64.1 + - - +
654B GLU* 3.4 14.4 + - - +
655B ASN* 3.1 24.4 + - - +
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Residues in contact with ASN 652 (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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204B ARG* 5.5 3.8 - - - +
371B TYR* 4.1 22.9 + - - -
373B GLY* 4.3 6.2 + - - -
589B SER* 5.5 0.9 - - - +
591B TYR* 3.4 49.2 + - + +
602B ALA* 5.7 2.0 - - - +
607B ARG* 3.0 30.0 - - - +
650B ASP* 3.1 4.4 + - - +
651B VAL* 1.3 77.6 - - - +
653B GLU* 1.3 69.0 + - - +
655B ASN* 2.9 18.3 + - - +
656B ASP* 2.9 12.1 + - - +
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Residues in contact with GLU 653 (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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576B ARG* 3.5 27.8 + - - +
579B ARG* 5.1 6.5 + - - +
589B SER* 3.0 22.2 + - - +
590B ILE* 3.1 20.4 - - + +
591B TYR* 3.8 11.2 - - - +
649B LEU* 3.0 40.6 - - + +
650B ASP* 2.7 18.2 + - - +
652B ASN* 1.3 75.3 - - - +
654B GLU* 1.3 54.1 + - - +
656B ASP* 2.8 8.7 + - - +
657B SER* 2.7 40.8 + - - -
672B HIS* 4.1 4.0 - - - -
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Residues in contact with GLU 654 (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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827A PHE* 4.8 2.9 - - + -
830A ARG* 4.5 0.2 + - - -
833A PRO* 4.2 24.9 - - + +
492B SER 4.5 6.9 - - - +
494B PHE 4.7 2.5 - - - +
496B MET* 3.1 31.0 - - - +
610B ARG* 3.8 23.8 + - - +
649B LEU* 3.7 17.7 - - + +
650B ASP 2.6 19.9 + - - +
651B VAL* 3.4 16.1 - - - +
653B GLU* 1.3 80.4 + - - +
655B ASN* 1.3 60.7 + - - +
657B SER* 2.8 31.3 + - - +
659B ILE* 4.1 18.5 - - + +
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Residues in contact with ASN 655 (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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827A PHE* 3.0 53.9 - - + +
828A GLN* 3.6 24.9 + - - +
830A ARG* 3.4 23.5 + - - +
837A LYS* 5.4 3.5 + - - -
371B TYR* 6.0 4.0 - - - -
651B VAL 3.1 21.1 + - - +
652B ASN* 2.9 10.4 + - - +
654B GLU* 1.3 78.5 - - - +
656B ASP* 1.3 59.5 + - - +
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Residues in contact with ASP 656 (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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830A ARG* 4.5 1.9 + - - -
837A LYS* 5.9 3.3 - - - +
572B VAL* 5.7 0.7 - - - +
576B ARG* 4.8 7.6 + - - +
590B ILE 5.5 0.2 - - - +
591B TYR* 3.3 19.5 - - + -
592B SER* 2.4 51.7 + - - +
652B ASN 2.9 5.0 + - - +
653B GLU 2.8 10.8 + - - +
655B ASN* 1.3 78.2 - - - +
657B SER* 1.3 61.2 + - - +
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Residues in contact with SER 657 (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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830A ARG* 2.6 33.6 + - - -
576B ARG* 6.1 0.2 - - - -
649B LEU* 4.7 2.2 - - - -
653B GLU* 2.7 30.8 + - - -
654B GLU* 2.8 21.5 + - - +
656B ASP* 1.3 75.1 - - - +
658B TYR* 1.3 54.4 + - - +
659B ILE* 4.6 1.6 - - - +
671B THR* 2.3 39.3 + - - -
672B HIS* 3.0 11.9 + - - -
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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