Contacts of the helix formed by residues 378 - 383 (chain D) in PDB entry 2VKM
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 378 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217D CYS* 4.9 1.0 - - - -
293D ASN* 4.5 5.3 + - - +
377D LEU* 1.3 82.9 - - + +
379D MET* 1.3 56.4 + - - +
380D GLU* 3.2 3.8 - - - +
381D ASP* 2.7 52.5 - - + +
382D CYS* 4.0 2.3 + - - -
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Residues in contact with MET 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D VAL* 3.5 25.1 - - + -
288D MET* 3.2 29.1 - - + +
293D ASN* 3.5 42.4 - - - +
294D GLN 3.5 14.6 - - - +
295D SER* 3.8 11.9 - - - -
376D THR* 2.9 28.3 - - - +
377D LEU 2.6 20.4 + - - +
378D ASP* 1.3 69.9 - - - +
380D GLU* 1.3 56.8 + - - +
381D ASP 2.8 5.8 - - - -
382D CYS* 2.8 36.3 + - - +
383D GLY 3.9 0.9 + - - -
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Residues in contact with GLU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ARG* 5.4 0.9 + - - -
202D ILE* 4.9 4.8 - - + +
218D LYS* 4.7 0.2 + - - -
288D MET* 3.6 13.1 - - + +
378D ASP* 3.2 1.9 - - - +
379D MET* 1.3 77.8 - - - +
381D ASP* 1.3 56.6 + - - +
382D CYS 3.1 1.3 - - - -
383D GLY* 3.3 19.7 + - - +
385D ASN* 5.7 1.2 + - - -
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Residues in contact with ASP 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ASP* 5.1 0.3 - - - +
217D CYS* 4.3 5.0 - - - -
218D LYS* 2.4 46.1 + - - +
378D ASP* 2.7 39.5 + - + +
380D GLU* 1.3 76.5 - - - +
382D CYS* 1.3 56.6 - - - +
383D GLY 3.1 2.0 - - - -
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Residues in contact with CYS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ILE* 3.6 14.6 - - + -
203D ILE 3.7 1.1 - - - +
204D VAL* 3.7 16.2 - - - -
217D CYS* 2.5 48.2 - - + -
218D LYS* 3.4 16.0 - - - +
221D ASN* 3.0 25.6 + - - +
377D LEU 5.1 1.1 - - - -
378D ASP 4.2 1.1 - - - -
379D MET* 2.8 36.8 + - - +
381D ASP* 1.3 77.6 - - - +
383D GLY* 1.3 62.8 + - - +
384D TYR 3.6 1.6 + - - -
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Residues in contact with GLY 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ARG* 3.7 12.3 - - - -
202D ILE* 3.6 23.8 - - - +
218D LYS* 3.2 23.2 + - - -
221D ASN* 5.0 2.0 - - - -
379D MET 3.9 0.8 + - - -
380D GLU 3.3 11.1 + - - +
381D ASP 3.1 1.2 - - - -
382D CYS* 1.3 79.5 - - - +
384D TYR* 1.3 63.4 + - - -
385D ASN* 3.8 7.3 + - - -
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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