Contacts of the helix formed by residues 833 - 842 (chain B) in PDB entry 2VF8
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 THR 833 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B HIS* 2.7 34.8 - - + +
529B THR* 3.4 17.4 + - - +
530B GLY* 3.8 3.4 - - - +
793B MET* 3.4 24.5 - - + +
804B ASP* 2.6 33.4 + - - +
825B VAL* 4.5 9.2 - - - +
831B SER* 3.1 5.1 + - - -
832B VAL* 1.3 79.3 - - + +
834B ALA* 1.3 64.7 + - - +
835B PRO 3.5 0.7 - - - -
836B TYR* 3.2 4.4 + - - -
837B LEU* 3.1 20.6 + - - +
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Residues in contact with ALA 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B VAL 4.0 15.7 - - - +
826B ALA* 3.6 14.6 - - - +
828B ALA 3.9 19.1 - - - +
831B SER* 3.1 34.4 + - - +
832B VAL 3.1 1.2 - - - -
833B THR* 1.3 78.2 - - - +
835B PRO* 1.3 66.8 - - + +
837B LEU 3.3 7.4 + - - -
838B ARG* 3.3 12.8 + - - +
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Residues in contact with PRO 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B SER 4.0 3.4 - - - +
832B VAL* 3.4 17.3 - - - +
834B ALA* 1.3 94.1 - - + +
836B TYR* 1.3 65.3 + - + +
838B ARG* 3.7 20.1 - - - +
839B ALA* 2.9 29.6 + - - +
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Residues in contact with TYR 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B HIS* 4.1 9.0 - - - -
414B PRO* 3.8 23.4 + - + -
415B ALA* 3.7 32.6 + - + -
793B MET* 3.4 22.6 - - + +
832B VAL* 3.5 23.8 - - + -
833B THR 3.2 6.5 + - - +
835B PRO* 1.3 85.4 - - + +
837B LEU* 1.3 57.8 + - - +
839B ALA* 3.6 8.9 - - + +
840B ALA* 3.1 26.5 + - - +
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Residues in contact with LEU 837 (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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793B MET* 3.9 20.0 - - + +
796B VAL* 3.4 35.4 - - + +
797B ALA* 4.2 18.6 - - + +
802B VAL* 4.4 2.2 - - + -
822B PRO* 3.8 26.2 - - + +
825B VAL* 4.2 14.1 - - + -
826B ALA* 3.5 19.7 - - + +
833B THR* 3.1 10.1 + - - +
834B ALA 3.7 4.5 - - - +
835B PRO 3.2 0.2 - - - -
836B TYR* 1.3 74.9 - - - +
838B ARG* 1.3 58.0 + - - +
839B ALA 3.1 0.9 - - - -
840B ALA* 2.8 3.5 + - + +
841B LEU* 2.6 48.0 + - + +
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Residues in contact with ARG 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B ALA* 3.2 29.3 + - + +
827B GLN* 3.1 30.3 - - - +
834B ALA* 3.3 5.5 + - - +
835B PRO* 3.7 25.6 - - - +
837B LEU* 1.3 79.1 - - - +
839B ALA* 1.3 65.7 + - - +
841B LEU* 3.3 10.2 + - - +
842B ARG* 3.4 31.4 + - + +
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Residues in contact with ALA 839 (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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489B ARG* 3.3 29.3 + - - +
835B PRO 2.9 20.2 + - - +
836B TYR* 3.6 12.8 - - + +
838B ARG* 1.3 79.8 - - - +
840B ALA* 1.3 59.0 + - + +
841B LEU 3.3 0.3 + - - -
842B ARG* 3.5 25.2 - - - +
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Residues in contact with ALA 840 (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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489B ARG* 3.4 22.1 + - - +
793B MET* 3.9 30.3 - - + +
794B GLN* 4.9 2.0 - - - +
797B ALA* 4.6 8.2 - - + +
836B TYR 3.1 15.0 + - - +
837B LEU* 2.8 9.0 + - + +
839B ALA* 1.3 73.6 - - - +
841B LEU* 1.3 66.7 + - - +
842B ARG 4.1 2.4 - - - +
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Residues in contact with LEU 841 (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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490B HIS 5.1 3.8 - - - +
491B THR* 5.3 1.4 - - - -
492B GLU 5.7 0.3 + - - -
493B PRO* 5.7 9.4 - - + +
494B HIS 6.1 2.7 - - - +
797B ALA* 4.0 31.2 - - + +
822B PRO* 3.8 26.7 - - + +
823B ALA* 3.8 19.7 - - + +
826B ALA* 4.1 13.2 - - + -
837B LEU* 2.6 24.2 + - + +
838B ARG* 3.8 5.4 - - - +
839B ALA 3.2 0.6 - - - -
840B ALA* 1.3 74.2 - - - +
842B ARG* 1.3 72.9 + - - +
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Residues in contact with ARG 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ARG* 3.3 62.5 + - + +
490B HIS 4.7 2.6 - - - +
491B THR* 3.0 37.5 - - - +
493B PRO* 6.0 0.5 - - - +
838B ARG* 3.4 23.9 + - + +
839B ALA* 3.5 31.0 + - - +
840B ALA 4.1 1.7 - - - +
841B LEU* 1.3 85.6 - - - +
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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