Contacts of the helix formed by residues 808 - 813 (chain B) in PDB entry 2NVT
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 808 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TRP* 3.9 9.8 - - + -
541B LEU* 3.8 21.4 - - + +
746B SER* 6.0 3.1 - - - +
747B MET* 5.3 0.2 - - + -
754B SER* 3.7 28.3 - - - -
806B THR* 2.7 16.5 + - + +
807B ARG* 1.3 73.1 - - - +
809B MET* 1.3 62.1 + - - +
810B GLU 3.3 0.2 - - - -
811B TYR* 3.6 13.3 + - - -
812B LEU* 3.3 26.9 + - - +
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Residues in contact with MET 809 (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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754B SER 4.3 8.1 - - - +
755B ILE* 3.6 20.0 - - + +
757B PRO* 5.5 0.4 - - + -
802B PRO* 4.2 2.7 - - - -
804B GLY 3.5 0.7 - - - +
805B THR* 3.4 36.1 - - - -
806B THR* 2.6 43.5 + - - +
808B ALA* 1.3 69.8 - - - +
810B GLU* 1.3 54.2 + - - +
812B LEU* 2.8 12.0 + - - +
813B LYS 2.7 32.1 + - - -
814B PHE* 3.1 40.4 + - + -
815B ARG* 4.1 11.0 - - - +
983B ARG* 3.5 25.6 - - - +
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Residues in contact with GLU 810 (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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35B SER* 4.9 3.1 + - - -
665B GLU* 5.0 6.2 - - - +
806B THR 4.1 1.0 + - - -
807B ARG* 3.6 23.1 + - - +
808B ALA 3.3 0.2 - - - -
809B MET* 1.3 79.0 - - - +
811B TYR* 1.3 85.3 + - + +
813B LYS* 3.1 21.2 + - - +
815B ARG* 4.2 19.1 - - + +
816B GLU* 3.5 19.1 - - - +
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Residues in contact with TYR 811 (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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31B TRP* 3.2 39.5 + + - +
34B ILE* 4.0 8.7 - - + -
35B SER* 2.9 43.1 + - - -
38B PHE* 4.1 44.8 - + + -
39B ARG* 5.2 1.8 - - - -
43B LEU* 3.2 25.3 - - - +
541B LEU* 5.4 2.5 - - + -
807B ARG* 3.5 23.4 + - - -
808B ALA* 4.1 10.3 - - + +
809B MET 3.3 0.2 - - - -
810B GLU* 1.3 95.1 + - + +
812B LEU* 1.3 64.6 + - + +
813B LYS* 3.2 7.9 - - - +
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Residues in contact with LEU 812 (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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38B PHE* 6.1 0.4 - - + -
43B LEU* 5.2 4.9 - - + -
488B TYR* 3.4 17.2 - - - -
489B SER* 3.9 13.2 - - - +
492B LEU* 3.5 22.2 - - + +
541B LEU* 3.8 27.8 - - + -
751B VAL* 3.4 44.4 - - + +
754B SER* 5.0 2.9 - - - -
755B ILE* 4.0 10.3 - - + -
808B ALA 3.3 21.2 + - - +
809B MET* 2.8 15.7 + - - +
811B TYR* 1.3 85.0 - - + +
813B LYS* 1.3 68.7 + - - +
814B PHE* 3.7 7.5 + - + +
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Residues in contact with LYS 813 (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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43B LEU* 5.7 2.5 - - + -
197B PHE* 3.7 32.6 - - + -
488B TYR* 3.8 21.0 - - + +
809B MET 2.7 5.5 + - - -
810B GLU* 3.1 15.8 + - - -
811B TYR* 4.4 8.5 - - - +
812B LEU* 1.3 83.4 - - - +
814B PHE* 1.3 54.2 + - - +
816B GLU* 3.2 37.7 + - - +
817B LEU* 3.2 26.2 + - - +
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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