Contacts of the helix formed by residues 690 - 694 (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 TYR 690 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B PRO* 1.3 84.9 - - + +
691B PRO* 1.3 71.4 - - - +
692B HIS* 3.1 26.2 + + - -
693B HIS* 3.2 31.9 + + + +
694B ASN* 4.4 1.7 + - - -
736B VAL* 5.2 3.4 - - + -
956B GLY* 4.0 15.8 - - - +
959B ILE* 4.2 20.2 - - + -
960B GLU* 4.7 9.9 - - - -
963B SER* 3.0 31.6 + - - -
975B TYR 3.1 17.6 + - - -
976B GLY* 3.8 21.3 - - - -
977B THR 4.3 7.4 - - - +
980B GLY 4.4 8.5 - - - -
982B SER* 3.4 25.0 + - - -
984B LEU* 6.5 0.4 - - + -
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Residues in contact with PRO 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A PHE* 4.3 11.4 - - + -
681B LEU* 3.7 32.5 - - + -
685B ALA 4.9 0.2 - - - +
688B ILE* 3.1 31.2 - - + +
689B PRO 3.3 2.4 - - - +
690B TYR* 1.3 89.4 - - - +
692B HIS* 1.3 56.3 + - - +
693B HIS 3.0 5.5 + - - -
694B ASN* 3.1 24.0 + - - +
699B ASN* 3.9 17.5 + - - +
738B THR* 6.3 0.2 - - + -
977B THR 4.1 0.4 - - - -
978B CYS* 3.9 28.3 - - + +
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Residues in contact with HIS 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A GLY* 3.6 16.9 - - - -
856A LEU* 3.1 43.6 + - + +
861A PHE* 4.6 10.8 - - - -
690B TYR* 3.8 16.4 - + - -
691B PRO* 1.3 77.7 - - - +
693B HIS* 1.3 94.2 + + - +
694B ASN 3.5 2.0 - - - +
977B THR 3.2 23.3 + - - -
978B CYS* 3.9 3.5 - - - -
979B PHE* 3.4 41.0 + - + +
980B GLY 3.8 14.2 + - - -
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Residues in contact with HIS 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A PHE* 2.8 37.2 - - - +
853A PHE* 2.9 24.4 + - - -
854A SER 4.3 0.6 - - - -
855A GLY* 3.8 5.3 + - - -
690B TYR* 3.7 15.3 - + - +
691B PRO 3.0 1.6 + - - -
692B HIS* 1.3 116.2 + + - +
694B ASN* 1.3 60.4 + - - +
953B MET 4.8 0.3 - - - +
954B THR* 4.7 0.3 - - - -
955B VAL* 3.3 24.8 + - + +
956B GLY* 3.6 21.8 - - - -
959B ILE* 3.4 27.9 - - + +
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Residues in contact with ASN 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A PHE* 3.0 21.8 - - - -
856A LEU* 5.2 1.7 - - - +
861A PHE* 5.7 2.8 - - - -
864A HIS* 3.8 5.7 - - - -
688B ILE* 4.0 9.5 - - - +
690B TYR 4.6 1.3 - - - -
691B PRO* 3.1 9.1 + - - +
692B HIS 4.6 2.4 - - - +
693B HIS* 1.3 78.4 - - - +
695B GLN* 1.3 63.2 + - - +
696B SER 4.1 0.4 + - - -
698B ARG* 4.8 3.5 - - + +
699B ASN* 3.4 31.6 + - - +
916B HIS* 2.5 40.1 + - - -
953B MET 4.6 1.8 - - - -
954B THR* 2.3 30.4 + - - +
956B GLY 3.4 7.6 + - - -
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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
------------------------------------------------------------
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