Contacts of the helix formed by residues 380 - 387 (chain C) in PDB entry 2WTV
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 HIS 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355C GLY* 3.4 26.9 - - - -
358C ASP* 2.8 27.5 + - + -
359C LEU* 3.6 27.7 + - + +
362C ARG* 4.4 11.9 - - - -
376C GLU 2.9 12.3 + - - +
377C VAL* 3.0 18.1 + - - +
379C GLU* 1.3 76.8 - - - +
381C PRO* 1.3 75.0 - - + +
382C TRP* 3.1 31.3 + - + +
383C ILE* 2.9 27.0 + - + +
384C THR* 2.9 11.3 + - - -
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Residues in contact with PRO 381 (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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355C GLY* 6.5 0.4 - - - -
379C GLU 3.5 5.3 - - - +
380C HIS* 1.3 104.2 - - + +
382C TRP* 1.3 56.1 + - - +
384C THR* 3.3 9.1 + - + +
385C ALA* 2.9 30.8 + - - +
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Residues in contact with TRP 382 (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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230C GLU* 2.8 50.6 + - + -
233C THR* 4.0 21.3 - - + -
234C ALA* 3.9 17.0 - - + -
237C ILE* 5.2 0.4 - - + -
319C CYS* 4.0 20.9 - - - -
323C LEU* 4.0 4.9 - - + -
353C THR* 3.9 3.4 - - - -
355C GLY* 3.5 24.0 - - - +
356C ALA* 3.3 30.5 - - + +
359C LEU* 4.1 10.3 - - + -
380C HIS* 3.1 14.5 + - + +
381C PRO* 1.3 76.5 - - - +
383C ILE* 1.3 91.4 + - + +
385C ALA* 4.6 2.0 - - - -
386C ASN* 3.1 47.3 + - - +
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Residues in contact with ILE 383 (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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234C ALA* 3.9 13.0 - - - +
237C ILE* 3.9 25.1 - - + -
238C THR* 3.3 23.3 - - + +
359C LEU* 4.1 8.3 - - + -
377C VAL* 3.4 22.2 - - + +
378C LEU* 3.8 20.6 - - - +
380C HIS* 2.9 16.2 + - + +
382C TRP* 1.3 106.2 - - + +
384C THR* 1.3 59.0 + - - +
387C SER* 3.0 37.0 + - - -
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Residues in contact with THR 384 (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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215B ARG* 3.6 11.8 + - - -
266B SER 4.7 1.9 - - - +
378C LEU 4.3 5.9 + - - -
379C GLU* 4.0 13.7 + - - -
380C HIS 2.9 11.7 + - - -
381C PRO* 3.6 12.3 - - + +
383C ILE* 1.3 78.7 - - - +
385C ALA* 1.3 62.9 + - + +
387C SER* 5.0 0.6 - - - +
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Residues in contact with ALA 385 (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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215B ARG* 3.0 28.2 + - - +
381C PRO 2.9 17.1 + - - +
382C TRP* 3.5 6.0 + - - +
383C ILE 3.2 0.2 - - - -
384C THR* 1.3 80.1 - - + +
386C ASN* 1.3 67.6 + - - +
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Residues in contact with ASN 386 (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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215B ARG* 3.2 14.1 + - - +
230C GLU* 3.8 31.4 + - + +
231C GLN* 3.1 25.2 + - - +
234C ALA* 3.6 14.6 - - + -
382C TRP* 3.1 47.6 + - + +
385C ALA* 1.3 88.8 - - - +
387C SER* 1.3 65.6 + - - +
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Residues in contact with SER 387 (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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215B ARG* 2.7 25.2 + - - +
267B ALA* 4.1 3.1 - - - +
234C ALA* 3.6 12.2 - - - +
235C THR* 3.6 10.2 - - - -
238C THR* 3.0 29.8 + - - -
383C ILE* 3.0 19.0 + - - -
384C THR* 5.0 1.0 - - - +
386C ASN* 1.3 77.2 - - - +
388C SER* 1.3 59.9 + - - +
389C LYS 3.0 25.6 + - - -
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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
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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