Contacts of the helix formed by residues 803 - 807 (chain B) in PDB entry 6WCZ
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 GLY 803 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ASN* 5.5 5.8 - - - -
801B GLY* 3.2 4.9 + - - -
802B LYS* 1.3 79.8 - - - +
804B GLU* 1.3 62.9 + - - +
805B TRP* 3.4 20.0 - - - +
806B MET* 3.8 21.5 - - - +
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Residues in contact with GLU 804 (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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766B LEU* 3.9 14.6 - - + +
802B LYS* 3.2 34.9 - - + +
803B GLY* 1.3 79.4 - - - +
805B TRP* 1.3 68.2 + - + +
806B MET 3.2 5.0 + - - -
807B THR* 4.3 11.8 + - - +
814B VAL* 3.2 35.5 - - - +
817B ARG* 5.3 3.3 - - - +
818B VAL* 3.3 31.5 - - + +
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Residues in contact with TRP 805 (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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513B LEU* 6.0 3.2 - - - +
759B SER* 4.0 16.2 - - - -
762B GLN* 3.2 38.5 - - + +
763B MET* 3.5 35.2 - - + +
766B LEU* 4.5 9.9 - - + -
767B LEU* 4.3 17.1 - - + +
791B PRO* 5.7 0.5 - - - +
793B GLY 6.0 2.0 - - - -
794B ARG* 5.8 0.9 - - - -
795B THR* 3.1 46.4 - - + -
796B THR* 5.2 2.0 - - - -
801B GLY* 5.5 8.0 - - - -
802B LYS* 5.3 3.2 - - - +
803B GLY* 4.6 15.0 - - - +
804B GLU* 1.3 97.1 - - + +
806B MET* 1.3 68.0 + - + +
807B THR* 3.5 4.4 + - - +
811B MET* 4.9 10.3 - - - -
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Residues in contact with MET 806 (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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406B SER* 6.0 3.6 - - - +
759B SER* 5.9 1.6 - - - +
790B VAL* 5.0 6.4 - - - +
791B PRO* 3.5 32.7 - - - +
792B THR* 4.8 13.9 - - - -
793B GLY 5.7 3.1 - - - +
803B GLY* 3.8 19.1 - - - +
804B GLU 3.2 2.6 + - - -
805B TRP* 1.3 85.7 - - + +
807B THR* 1.3 67.2 + - - +
808B THR* 4.9 0.9 + - - -
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Residues in contact with THR 807 (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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762B GLN* 4.0 14.9 + - - -
791B PRO* 4.4 6.9 - - - +
804B GLU 4.3 9.7 + - - +
805B TRP 4.5 1.2 - - - +
806B MET* 1.3 84.4 - - - +
808B THR* 1.3 68.0 + - - +
809B GLU* 2.9 32.0 + - + +
811B MET* 3.8 19.5 - - + -
814B VAL* 3.8 11.2 - - + -
817B ARG* 6.1 0.4 - - - +
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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