Contacts of the helix formed by residues 365 - 378 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PRO* 5.0 2.8 - - - +
343B ILE* 4.7 0.7 - - - +
345B ARG* 5.1 3.2 + - - +
362B GLN 5.6 0.2 - - - +
364B GLY* 1.3 74.0 - - - +
366B VAL* 1.3 60.9 + - - +
367B VAL* 2.9 29.0 + - - +
368B HIS* 3.2 22.8 + - + +
369B GLY* 2.9 27.2 + - - -
1393B AR6 3.2 27.0 + - - -
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY 3.6 23.1 - - - +
148B ILE* 4.4 5.2 - - + -
151B PRO* 3.8 14.8 - - + -
209B THR* 3.8 30.3 - - + +
318B LEU* 4.4 10.5 - - + -
319B GLY 4.7 1.8 - - - +
343B ILE* 4.0 30.1 - - + +
365B ASP* 1.3 73.3 - - - +
367B VAL* 1.3 61.3 + - - +
369B GLY* 3.4 0.9 + - - -
370B VAL* 2.9 30.4 + - + +
1393B AR6 2.8 27.0 + - + +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PRO* 3.8 31.9 - - + -
207B ASN* 3.9 16.2 - - + +
208B VAL* 4.6 12.6 - - + +
209B THR* 4.0 7.9 - - - +
365B ASP* 2.9 12.7 + - - +
366B VAL* 1.3 73.7 - - - +
368B HIS* 1.3 59.6 + - - +
370B VAL* 3.3 5.1 + - - +
371B GLU* 2.8 57.9 + - + +
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 4.9 10.0 + - - -
364B GLY* 6.2 0.8 - - - -
365B ASP* 3.2 26.3 + - + +
367B VAL* 1.3 76.5 - - - +
369B GLY* 1.3 61.0 + - - +
371B GLU* 3.7 11.8 - - + +
372B SER* 2.8 49.8 + - - -
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.5 3.1 - - - +
343B ILE* 3.8 20.9 - - - +
362B GLN* 4.0 19.7 - - - -
365B ASP 2.9 16.7 + - - -
366B VAL 3.7 1.6 - - - -
368B HIS* 1.3 78.3 + - - +
370B VAL* 1.3 60.4 + - - +
372B SER* 3.3 6.3 + - - -
373B LEU* 3.1 21.3 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.2 17.9 - - + +
209B THR* 4.2 23.8 - - + -
212B PHE* 3.6 41.5 - - + -
318B LEU* 4.9 4.0 - - + -
343B ILE* 4.2 15.9 - - + -
366B VAL* 2.9 27.6 + - + +
367B VAL* 3.9 4.9 - - - +
369B GLY* 1.3 69.7 - - - +
371B GLU* 1.3 60.3 + - - +
373B LEU* 3.2 7.5 + - - +
374B VAL* 2.8 33.3 + - + +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.1 28.1 - - + +
367B VAL* 2.8 40.6 + - - +
368B HIS* 3.7 11.7 - - + +
370B VAL* 1.3 71.8 - - - +
372B SER* 1.3 57.9 + - - +
374B VAL* 3.6 7.8 - - + +
375B GLU* 2.9 31.4 + - - +
380B THR* 5.1 0.2 + - - -
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.9 17.5 - - - -
362B GLN* 5.0 4.4 + - - -
368B HIS* 2.8 36.2 + - - -
369B GLY* 3.4 11.8 - - - -
370B VAL 3.2 0.2 - - - -
371B GLU* 1.3 75.9 - - - +
373B LEU* 1.3 56.9 + - - +
375B GLU* 3.3 8.0 + - - +
376B LEU* 3.0 34.1 + - - +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.1 25.0 - - + +
128B VAL* 5.0 2.7 - - + -
129B ALA* 4.0 28.9 - - + +
132B ILE* 5.3 5.4 - - + -
212B PHE* 3.7 27.4 - - + -
316B LEU* 5.0 5.6 - - + -
341B LEU* 3.9 24.2 - - + -
343B ILE* 4.1 11.2 - - + -
369B GLY 3.1 9.4 + - - +
370B VAL* 3.7 8.3 - - - +
372B SER* 1.3 75.7 - - - +
374B VAL* 1.3 59.8 + - - +
376B LEU* 3.2 3.4 + - - +
377B LEU* 2.8 47.4 + - + +
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 5.8 1.1 - - + -
212B PHE* 3.6 29.6 - - + -
370B VAL* 2.8 28.8 + - + +
371B GLU* 3.6 10.1 - - + +
373B LEU* 1.3 72.5 - - - +
375B GLU* 1.3 63.7 + - - +
377B LEU* 3.2 8.2 + - - +
378B GLY 3.1 3.6 + - - -
379B TRP* 3.0 33.0 + - + -
380B THR* 3.7 23.6 - - + +
383B MET* 3.6 33.4 - - + -
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 5.2 1.6 + - - -
371B GLU 2.9 17.3 + - - +
372B SER* 3.6 7.6 - - - +
373B LEU 3.2 0.2 - - - -
374B VAL* 1.3 78.3 - - - +
376B LEU* 1.3 60.3 + - + +
378B GLY* 2.9 19.8 + - - -
380B THR* 2.7 37.5 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.3 20.0 + - - +
241A ALA* 6.1 2.7 - - + +
125B LEU* 3.8 24.2 - - + -
126B GLN* 3.8 53.6 - - + +
129B ALA* 3.6 22.2 - - + +
130B GLU* 4.0 2.9 - - - +
133B ARG* 3.8 3.3 - - - -
372B SER* 3.0 22.1 + - - +
373B LEU 3.7 2.2 - - - +
375B GLU* 1.3 78.3 - - + +
377B LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ARG* 4.7 0.2 - - - -
266A GLU* 4.7 1.9 - - - +
129B ALA* 3.4 35.4 - - + +
132B ILE* 3.7 27.1 - - + -
133B ARG* 3.6 26.6 + - + +
212B PHE* 3.8 16.2 - - + -
373B LEU* 2.8 31.6 + - + +
374B VAL* 3.6 6.3 - - - +
375B GLU 3.1 0.4 - - - -
376B LEU* 1.3 79.6 - - - +
378B GLY* 1.3 58.5 + - - +
379B TRP* 3.5 51.7 + - + -
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 4.9 7.9 - - - -
252A ALA 5.6 2.7 - - - +
264A PRO* 6.0 1.4 - - - +
266A GLU* 6.0 0.7 - - - +
133B ARG* 5.5 0.2 - - - -
375B GLU 2.9 15.3 + - - -
376B LEU 3.2 1.2 + - - -
377B LEU* 1.3 79.3 - - - +
379B TRP* 1.3 64.0 + - - +
380B THR* 3.5 3.5 + - - -
381B GLU 5.3 0.3 + - - -
382B GLU* 4.1 7.6 - - - +
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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