Contacts of the helix formed by residues 365 - 378 (chain C) in PDB entry 4BVH
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 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C PRO* 4.8 2.4 - - - +
343C ILE* 4.6 1.2 - - - +
345C ARG* 5.4 2.7 + - - +
364C GLY* 1.3 73.5 - - - -
366C VAL* 1.3 59.5 + - - +
367C VAL* 3.0 28.5 + - - +
368C HIS* 3.1 25.1 + - + +
369C GLY* 2.9 24.8 + - - -
1395C OAD 3.1 27.9 + - - -
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLY 3.7 19.1 - - - +
148C ILE* 4.5 5.6 - - + -
151C PRO* 3.9 15.9 - - + -
209C THR* 4.0 18.6 - - + +
318C LEU* 4.1 21.5 - - + -
319C GLY 4.6 2.0 - - - +
343C ILE* 4.0 30.5 - - + +
364C GLY 4.3 0.2 - - - -
365C ASP* 1.3 70.1 - - - +
367C VAL* 1.3 64.9 + - - +
369C GLY 3.8 0.2 - - - -
370C VAL* 2.9 27.3 + - - +
1395C OAD 2.8 34.5 + - + +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C PRO* 3.7 34.5 - - + -
207C ASN* 3.9 16.4 - - + +
208C VAL* 4.3 15.4 - - + +
209C THR* 4.0 5.6 - - - +
365C ASP* 3.0 10.3 + - - +
366C VAL* 1.3 77.9 - - - +
368C HIS* 1.3 54.6 + - - +
370C VAL* 3.3 4.7 + - - +
371C GLU* 2.8 59.0 + - + +
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Residues in contact with HIS 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 4.7 11.4 + - - -
364C GLY* 6.1 1.4 - - - -
365C ASP* 3.1 28.3 + - + +
366C VAL 3.4 0.2 - - - -
367C VAL* 1.3 76.2 - - - +
369C GLY* 1.3 59.4 + - - +
371C GLU* 3.3 14.5 + - + +
372C SER* 2.9 50.1 + - - -
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Residues in contact with GLY 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 4.4 3.6 - - - +
343C ILE* 3.9 13.9 - - - +
362C GLN* 3.9 23.1 - - - +
365C ASP 2.9 17.0 + - - -
366C VAL 3.4 1.3 + - - -
367C VAL 3.3 0.4 - - - -
368C HIS* 1.3 80.5 + - - +
370C VAL* 1.3 60.9 + - - +
372C SER* 3.3 6.1 + - - -
373C LEU* 3.1 22.3 + - - +
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Residues in contact with VAL 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 4.0 19.5 - - + +
209C THR* 4.3 12.3 - - + +
212C PHE* 3.6 39.0 - - + -
318C LEU* 3.6 31.0 - - + -
343C ILE* 4.2 8.2 - - + +
366C VAL* 2.9 21.8 + - + +
367C VAL* 3.7 5.2 - - - +
369C GLY* 1.3 76.0 - - - +
371C GLU* 1.3 57.1 + - - +
373C LEU* 3.2 7.7 + - - +
374C VAL* 2.9 31.1 + - + +
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Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 4.0 24.8 - - + +
367C VAL* 2.8 42.4 + - - +
368C HIS* 3.8 13.5 - - + +
370C VAL* 1.3 71.7 - - - +
372C SER* 1.3 57.1 + - - +
374C VAL* 3.4 9.3 + - + +
375C GLU* 3.0 30.4 + - - +
380C THR* 4.9 0.9 + - - -
383C MET* 6.3 1.8 - - + -
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Residues in contact with SER 372 (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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125C LEU* 3.9 17.3 - - - -
362C GLN* 5.0 4.0 - - - -
368C HIS* 2.9 39.5 + - - -
369C GLY* 3.6 10.8 - - - -
370C VAL 3.3 0.2 - - - -
371C GLU* 1.3 76.5 - - - +
373C LEU* 1.3 57.2 + - - +
375C GLU* 3.3 7.7 + - - +
376C LEU* 3.0 32.5 + - - +
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Residues in contact with LEU 373 (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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125C LEU* 3.8 29.3 - - + +
128C VAL* 4.9 2.5 - - + -
129C ALA* 3.9 28.5 - - + +
132C ILE* 4.8 7.9 - - + -
212C PHE* 3.7 27.6 - - + -
316C LEU* 5.0 4.3 - - + -
341C LEU* 3.9 23.3 - - + -
343C ILE* 4.4 9.4 - - + -
369C GLY 3.1 12.2 + - - +
370C VAL* 3.2 9.2 + - - +
372C SER* 1.3 72.4 - - - +
374C VAL* 1.3 54.8 + - - +
376C LEU* 3.0 3.7 + - - +
377C LEU* 2.7 48.3 + - + +
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Residues in contact with VAL 374 (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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208C VAL* 6.0 0.7 - - + -
212C PHE* 3.5 33.2 - - + -
370C VAL* 2.9 27.3 + - + +
371C GLU* 3.6 8.7 - - + +
373C LEU* 1.3 73.9 - - - +
375C GLU* 1.3 61.8 + - - +
377C LEU* 3.2 9.4 + - + +
378C GLY 3.1 4.2 + - - -
379C TRP* 2.9 56.4 + - + +
380C THR* 3.6 13.0 - - + +
383C MET* 4.0 21.1 - - + -
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Residues in contact with GLU 375 (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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371C GLU 3.0 17.8 + - - +
372C SER* 3.6 7.6 - - - +
374C VAL* 1.3 74.9 - - - +
376C LEU* 1.3 67.5 + - + +
378C GLY* 3.0 14.9 + - - -
380C THR* 2.7 37.4 + - - +
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 3.7 33.2 - - + -
126C GLN* 3.8 42.9 - - + +
129C ALA* 3.5 22.4 - - + +
130C GLU* 4.0 13.2 - - - +
133C ARG* 4.6 2.6 - - - -
372C SER* 3.0 19.8 + - - +
373C LEU 3.0 4.7 + - - +
375C GLU* 1.3 81.5 - - + +
377C LEU* 1.3 61.0 + - - +
378C GLY 3.4 0.9 + - - -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 3.3 32.1 - - + +
132C ILE* 3.6 27.6 - - + -
133C ARG* 3.9 27.2 + - + +
212C PHE* 3.7 21.5 - - + -
373C LEU* 2.7 32.8 + - + +
374C VAL* 3.4 9.6 - - - +
375C GLU 3.2 0.2 - - - -
376C LEU* 1.3 74.5 - - - +
378C GLY* 1.3 56.9 + - - +
379C TRP* 3.4 51.0 + - + -
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Residues in contact with GLY 378 (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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133C ARG* 5.9 0.7 - - - -
375C GLU* 3.0 16.4 + - - -
376C LEU 3.3 1.2 + - - -
377C LEU* 1.3 79.0 - - - +
379C TRP* 1.3 64.3 + - - +
380C THR 3.5 3.1 - - - -
381C GLU* 3.8 10.9 - - - +
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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