Contacts of the helix formed by residues 440 - 445 (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 ASP 440 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C SER* 2.9 22.0 + - - +
412C LEU* 5.9 0.2 - - - +
417C THR* 4.6 9.0 + - - -
438C GLU* 3.4 20.5 + - + +
439C HIS* 1.3 75.0 - - - +
441C LEU* 1.3 63.0 + - - +
442C ASP* 2.9 41.0 + - - +
443C VAL* 3.0 21.4 + - + +
444C ILE* 2.8 19.2 + - - +
792C LYS* 3.7 16.6 - - - +
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Residues in contact with LEU 441 (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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439C HIS 3.2 5.0 + - - +
440C ASP* 1.3 72.3 + - - +
442C ASP* 1.3 58.2 + - - +
443C VAL 3.1 0.2 - - - -
444C ILE* 3.5 12.5 - - + +
445C ARG* 3.1 49.7 + - - +
481C THR* 4.7 7.6 - - + +
484C TYR* 4.1 40.8 - - + +
485C LEU* 4.2 23.9 - - + +
765C HIS* 5.8 0.7 - - + +
766C PRO* 4.0 28.0 - - + -
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Residues in contact with ASP 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C PRO* 5.8 4.2 - - - +
417C THR* 4.3 14.9 - - + +
421C LEU* 3.9 8.1 - - - +
440C ASP* 2.9 14.1 + - - +
441C LEU* 1.3 77.9 + - - +
443C VAL* 1.3 59.7 + - - +
445C ARG* 3.7 23.4 + - - +
446C ARG* 3.8 19.8 - - - +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.8 2.7 - - + +
40C VAL* 4.8 9.4 - - + -
408C PRO* 6.1 0.2 - - + -
409C SER* 5.0 1.3 - - - -
417C THR* 4.3 13.2 - - + +
420C LEU* 4.4 18.6 - - + -
421C LEU* 4.0 24.1 - - + +
424C LEU* 4.8 12.8 - - + -
436C VAL* 5.5 3.4 - - + -
438C GLU* 4.1 24.5 - - + +
440C ASP* 3.0 24.4 + - + +
442C ASP* 1.3 82.2 - - - +
444C ILE* 1.3 65.4 + - - +
445C ARG 3.3 1.3 - - - -
446C ARG* 3.1 14.0 + - - +
447C ALA* 3.4 9.9 + - - +
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Residues in contact with ILE 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.6 24.5 - - + -
42C THR* 3.6 20.9 - - + -
438C GLU* 3.4 32.5 - - + +
439C HIS* 4.2 2.9 - - - +
440C ASP 2.8 27.9 + - - +
441C LEU* 3.5 19.7 - - + +
443C VAL* 1.3 76.1 - - - +
445C ARG* 1.3 61.1 + - - +
446C ARG 3.1 1.4 + - - -
447C ALA* 3.2 17.4 + - - +
450C LEU* 3.9 21.5 - - + -
470C PRO* 3.8 8.9 - - + +
481C THR* 4.6 6.7 - - + -
485C LEU* 4.4 13.0 - - + -
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Residues in contact with ARG 445 (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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441C LEU* 3.1 35.7 + - - +
442C ASP* 3.7 29.4 + - - +
443C VAL 3.3 0.2 - - - -
444C ILE* 1.3 75.5 - - - +
446C ARG* 1.3 65.4 + - + +
447C ALA 3.4 3.7 - - - +
470C PRO* 4.6 10.0 - - - +
484C TYR 5.2 0.8 + - - -
485C LEU* 3.5 50.2 + - + +
486C PHE* 6.2 3.4 - - + -
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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