Contacts of the helix formed by residues 833 - 842 (chain C) in PDB entry 2VF7
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C HIS* 3.0 25.6 + - - +
529C THR* 4.2 12.5 - - + +
530C GLY* 4.3 1.2 - - - -
793C MET* 3.8 31.6 - - + -
804C ASP* 2.6 32.8 + - - -
825C VAL* 5.1 3.6 - - + -
831C SER* 3.4 0.8 + - - -
832C VAL* 1.3 79.7 - - - +
834C ALA* 1.3 66.5 + - - +
835C PRO 3.4 0.4 - - - -
836C TYR* 2.9 6.0 + - - -
837C LEU* 2.9 34.5 + - + -
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Residues in contact with ALA 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C VAL* 3.3 28.2 - - - +
826C ALA* 3.6 17.0 - - - +
828C ALA 3.6 19.7 - - - +
831C SER* 3.7 10.6 + - - +
833C THR* 1.3 77.5 - - - +
835C PRO* 1.4 71.2 - - + +
837C LEU* 3.3 3.3 + - - +
838C ARG* 3.0 28.4 + - - +
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Residues in contact with PRO 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831C SER 3.7 11.4 - - - +
832C VAL* 3.9 8.1 - - - +
833C THR 3.6 3.6 - - - -
834C ALA* 1.4 95.6 - - + +
836C TYR* 1.3 69.3 + - + +
838C ARG* 3.6 29.3 + - - +
839C ALA* 3.3 21.5 + - - +
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Residues in contact with TYR 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C HIS* 4.4 7.4 - + + -
414C PRO* 3.8 34.5 + - + -
415C ALA* 3.8 30.3 + - + +
793C MET* 4.2 12.4 - - + +
832C VAL* 3.3 28.3 - - + -
833C THR* 2.9 6.1 + - - +
835C PRO* 1.3 82.6 - - + +
837C LEU* 1.3 66.0 + - - +
839C ALA* 3.4 6.9 + - + +
840C ALA* 3.2 20.6 + - - +
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Residues in contact with LEU 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793C MET* 3.7 14.8 - - + +
796C VAL* 4.2 19.7 - - + -
797C ALA* 3.8 34.8 - - + +
802C VAL* 4.9 2.7 - - + -
822C PRO* 3.4 29.2 - - + +
825C VAL* 4.0 18.2 - - + -
826C ALA* 4.0 10.8 - - + +
833C THR* 2.9 21.8 + - + +
834C ALA 3.7 3.6 - - - +
836C TYR* 1.3 76.9 - - - +
838C ARG* 1.3 56.0 + - - +
840C ALA* 2.9 7.4 + - - +
841C LEU* 2.9 36.6 + - + +
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Residues in contact with ARG 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C ALA* 3.3 28.5 + - + +
827C GLN* 3.9 23.4 + - - +
834C ALA* 3.0 15.2 + - - +
835C PRO* 3.6 37.3 + - - +
837C LEU* 1.3 77.4 - - - +
839C ALA* 1.3 59.9 + - - +
841C LEU* 3.3 28.3 + - + +
842C ARG* 4.0 3.8 + - - +
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Residues in contact with ALA 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C PRO 3.3 11.2 + - - +
836C TYR* 3.9 9.4 - - + +
837C LEU 3.3 0.6 - - - -
838C ARG* 1.3 78.9 - - - +
840C ALA* 1.3 57.2 + - - +
842C ARG* 3.0 32.5 + - - +
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Residues in contact with ALA 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLY 4.6 1.7 - - - +
793C MET* 3.9 26.7 - - + +
794C GLN* 5.9 0.2 - - - -
797C ALA* 4.1 17.2 - - + +
836C TYR 3.2 11.5 + - - +
837C LEU 2.9 11.8 + - - +
839C ALA* 1.3 77.4 - - - +
841C LEU* 1.3 62.1 + - - +
842C ARG* 3.5 2.8 + - - +
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Residues in contact with LEU 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY* 2.9 33.6 - - - +
134B GLN* 3.7 6.3 - - - +
135B GLY* 4.0 25.8 - - - +
797C ALA* 4.1 6.3 - - + +
822C PRO* 4.0 20.9 - - + +
823C ALA* 4.2 9.6 - - + +
826C ALA* 3.6 30.5 - - + -
827C GLN* 5.9 0.4 - - - +
837C LEU* 2.9 24.6 + - + +
838C ARG* 3.3 19.3 - - + +
839C ALA 3.3 0.2 - - - -
840C ALA* 1.3 78.4 - - - +
842C ARG* 1.3 73.2 + - - +
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Residues in contact with ARG 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLN* 4.5 10.4 + - - -
135B GLY* 3.9 13.1 + - - -
298B GLU* 5.6 0.5 - - - +
488C ASP* 6.1 0.9 - - - -
490C HIS* 3.2 32.9 + - + +
492C GLU* 3.8 9.7 - - - +
838C ARG 4.0 3.2 + - - +
839C ALA* 3.0 26.3 + - - +
840C ALA 4.6 3.0 - - - +
841C LEU* 1.3 91.2 - - - +
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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