Contacts of the helix formed by residues 851 - 860 (chain A) in PDB entry 6WCW
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 SER 851 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785A TRP 3.3 11.0 - - - -
786A ASN* 3.6 9.0 + - - -
787A ASP 3.0 31.4 - - - -
788A PRO* 4.0 1.3 - - - -
790A PHE* 4.4 2.2 - - - -
842A HIS* 4.1 2.7 + - - -
850A TYR* 1.3 74.3 - - - +
852A LEU* 1.3 64.2 + - - +
853A ASN* 3.6 7.4 + - - +
854A ASP* 2.8 36.7 + - - -
855A LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 852 (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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757A ALA* 5.8 5.6 - - + +
758A ILE 5.5 0.4 - - - -
759A PRO* 4.5 26.7 - - + -
762A VAL* 5.4 10.1 - - + -
781A LEU* 4.2 16.2 - - + +
784A ILE* 4.1 29.4 - - + +
785A TRP* 3.3 40.2 + - + +
787A ASP 4.6 0.2 + - - -
790A PHE* 3.8 22.4 - - + -
851A SER* 1.3 74.7 - - - +
853A ASN* 1.3 62.6 + - - +
855A LEU* 3.4 12.4 + - + +
856A THR* 3.0 28.8 + - - -
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Residues in contact with ASN 853 (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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785A TRP* 3.2 26.4 + - + +
786A ASN* 2.9 32.5 + - - +
840A PRO* 5.8 4.0 - - - +
851A SER* 3.1 9.2 - - - +
852A LEU* 1.3 75.9 - - - +
854A ASP* 1.3 63.5 + - - +
856A THR* 3.4 2.3 + - - -
857A ALA* 2.8 34.0 + - - +
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Residues in contact with ASP 854 (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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840A PRO* 4.1 18.5 - - - +
842A HIS* 2.7 31.1 + - - -
843A LEU* 4.2 12.0 - - - +
850A TYR* 3.8 15.2 - - + -
851A SER* 2.8 26.0 + - - +
853A ASN* 1.3 78.7 + - - +
855A LEU* 1.3 58.7 + - - +
857A ALA* 3.7 3.5 - - - -
858A THR* 2.5 40.1 + - - -
863A LEU* 3.7 19.3 - - + +
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Residues in contact with LEU 855 (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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762A VAL* 4.3 20.2 - - + -
763A LEU* 3.8 24.9 - - + -
766A TRP* 3.8 21.9 - - + -
768A PHE* 3.6 12.2 - - + -
790A PHE* 4.7 11.2 - - + -
792A VAL* 4.8 6.5 - - + -
806A LEU* 4.3 7.9 - - + -
850A TYR* 3.6 35.0 - - + -
851A SER 3.0 20.1 + - - +
852A LEU* 3.8 12.8 - - + +
854A ASP* 1.3 79.3 - - - +
856A THR* 1.3 61.3 + - - +
858A THR* 3.4 4.7 + - - -
859A ARG 3.1 16.3 + - - -
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Residues in contact with THR 856 (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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768A PHE* 3.6 20.5 - - - -
785A TRP* 3.8 24.2 - - + -
852A LEU* 3.0 17.7 + - - +
853A ASN* 3.9 3.8 - - - -
855A LEU* 1.3 75.0 - - - +
857A ALA* 1.3 53.8 + - - +
859A ARG* 2.8 47.9 + - - +
860A LYS* 2.8 30.5 + - + +
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Residues in contact with ALA 857 (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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853A ASN* 2.8 29.3 + - - +
854A ASP* 3.9 5.4 - - - +
856A THR* 1.3 73.2 - - - +
858A THR* 1.3 58.8 + - - +
860A LYS* 3.9 2.7 - - - -
861A GLY 3.2 2.1 + - - -
862A GLU* 2.9 57.0 + - + +
863A LEU* 3.3 16.9 + - + -
866A ARG* 5.5 3.6 - - - +
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Residues in contact with THR 858 (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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766A TRP* 4.4 5.2 - - + -
805A LEU* 3.3 50.9 - - + +
806A LEU* 3.8 21.6 - - + +
809A VAL* 4.2 11.6 - - + +
850A TYR* 4.7 1.0 - - - -
854A ASP 2.5 26.6 + - - -
855A LEU* 3.5 8.5 - - - -
857A ALA* 1.3 71.4 - - - +
859A ARG* 1.3 61.3 + - - +
861A GLY* 2.9 15.5 + - - -
863A LEU* 3.4 21.9 - - - +
864A GLY 5.6 0.4 - - - +
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Residues in contact with ARG 859 (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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766A TRP* 3.8 28.7 - - + +
768A PHE* 3.6 42.7 - - + +
805A LEU* 4.1 9.4 - - - +
855A LEU 3.1 11.7 + - - +
856A THR* 2.8 38.7 + - - +
858A THR* 1.3 69.1 - - - +
860A LYS* 1.3 80.1 + - - +
861A GLY* 2.9 10.8 + - - -
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Residues in contact with LYS 860 (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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856A THR* 2.8 29.6 + - + +
857A ALA* 4.0 3.6 - - - +
859A ARG* 1.3 98.5 - - - +
861A GLY* 1.3 61.6 + - - +
862A GLU* 3.3 28.1 + - + +
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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