Contacts of the helix formed by residues 365 - 378 (chain A) in PDB entry 4BN4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A PRO* 5.2 1.0 - - - +
343A ILE* 4.8 0.3 - - - +
345A ARG* 5.3 2.0 + - - +
364A GLY* 1.3 74.3 - - - -
366A VAL* 1.3 58.7 + - - +
367A VAL* 2.8 31.1 + - - +
368A HIS* 3.1 24.2 + - + +
369A GLY* 2.9 26.0 + - - -
1395A AR6 3.1 28.4 + - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY 3.7 19.7 - - - +
148A ILE* 4.5 10.5 - - + -
151A PRO* 3.8 19.7 - - + -
209A THR* 4.0 25.4 - - + +
318A LEU* 4.7 2.7 - - + -
319A GLY* 4.7 3.1 - - - +
343A ILE* 4.0 31.2 - - + +
365A ASP* 1.3 71.9 - - - +
367A VAL* 1.3 60.2 + - - +
369A GLY* 3.8 0.2 - - - -
370A VAL* 2.9 37.9 + - + +
1395A AR6 2.9 29.4 + - + +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.5 36.1 - - + -
207A ASN* 4.2 0.9 - - + +
208A VAL* 3.6 23.6 - - + -
209A THR* 4.1 7.9 - - - +
365A ASP* 2.8 13.1 + - - +
366A VAL* 1.3 75.9 - - - +
368A HIS* 1.3 57.9 + - - +
370A VAL* 3.4 1.6 + - - +
371A GLU* 2.8 61.4 + - - +
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Residues in contact with HIS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLN* 4.4 14.9 + - - -
363A LEU 5.8 1.4 + - - -
364A GLY* 6.0 1.4 - - - -
365A ASP* 3.1 28.4 + - + +
367A VAL* 1.3 74.9 - - - +
369A GLY* 1.3 60.4 + - - +
371A GLU* 3.3 10.9 + - + +
372A SER* 2.8 50.3 + - - -
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Residues in contact with GLY 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.5 3.3 - - - +
343A ILE* 4.0 15.0 - - - +
362A GLN* 3.9 22.9 - - - -
365A ASP 2.9 14.6 + - - -
366A VAL 3.8 2.2 - - - -
367A VAL 3.2 0.2 - - - -
368A HIS* 1.3 81.3 + - - +
370A VAL* 1.3 60.5 + - - +
372A SER* 3.3 5.4 + - - -
373A LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.3 14.4 - - + +
209A THR* 4.2 25.8 - - + +
212A PHE* 3.7 39.7 - - + -
318A LEU* 5.1 4.5 - - + -
343A ILE* 4.3 15.2 - - + +
366A VAL* 2.9 27.7 + - + +
367A VAL* 3.9 4.0 - - - +
369A GLY* 1.3 72.6 - - - +
371A GLU* 1.3 60.2 + - + +
373A LEU* 3.2 7.4 + - - +
374A VAL* 2.8 33.6 + - + +
383A MET* 5.2 1.6 - - + -
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.1 20.9 - - + +
367A VAL* 2.8 46.3 + - + +
368A HIS* 3.8 8.0 - - + +
370A VAL* 1.3 74.7 - - + +
372A SER* 1.3 57.7 + - - +
374A VAL* 3.6 8.5 - - + +
375A GLU* 2.9 30.1 + - - +
380A THR* 4.9 0.5 + - - -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 16.2 - - - -
362A GLN* 4.7 3.7 + - - -
368A HIS* 2.8 44.3 + - - -
369A GLY* 3.5 7.2 - - - -
370A VAL 3.2 0.2 - - - -
371A GLU* 1.3 73.8 - - - +
373A LEU* 1.3 64.4 + - - +
375A GLU* 3.3 6.2 + - - +
376A LEU* 3.0 28.5 + - - +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 24.8 - - + +
128A VAL 4.9 0.7 - - - -
129A ALA* 3.8 32.3 - - + +
132A ILE* 4.9 8.5 - - + -
212A PHE* 3.7 29.8 - - + -
316A LEU* 4.9 6.7 - - + -
341A LEU* 4.1 22.2 - - + -
343A ILE* 4.5 8.7 - - + -
369A GLY 3.0 14.0 + - - +
370A VAL* 3.6 9.0 - - - +
372A SER* 1.3 74.8 - - - +
374A VAL* 1.4 64.9 + - - +
376A LEU* 3.2 3.9 + - - -
377A LEU* 2.9 37.3 + - + +
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 3.6 30.7 - - + -
370A VAL* 2.8 30.6 + - + +
371A GLU* 3.6 9.0 - - + +
373A LEU* 1.4 73.9 - - - +
375A GLU* 1.3 63.7 + - - +
377A LEU* 3.2 9.4 + - + +
378A GLY 3.2 3.8 + - - -
379A TRP* 3.0 51.9 + - + -
380A THR* 3.6 11.7 - - + +
383A MET* 3.6 24.9 - - + -
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A GLU 2.9 17.4 + - - +
372A SER* 3.8 6.7 - - - +
374A VAL* 1.3 78.1 - - - +
376A LEU* 1.3 64.3 + - + +
378A GLY* 3.0 14.4 + - - -
380A THR* 2.6 37.9 + - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.7 33.7 - - + -
126A GLN* 3.8 42.1 - - + +
129A ALA* 3.5 18.4 - - + +
130A GLU* 3.7 19.2 - - - +
133A ARG* 4.4 2.3 - - - -
372A SER* 3.0 20.5 + - - +
373A LEU* 3.6 4.5 - - - +
375A GLU* 1.3 80.4 - - + +
377A LEU* 1.4 57.1 + - - +
378A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 3.3 32.1 - - + +
132A ILE* 3.7 26.9 - - + -
133A ARG* 3.5 28.3 + - + +
212A PHE* 3.7 31.6 - - + -
373A LEU* 2.9 30.1 + - + +
374A VAL* 3.2 9.6 + - - +
376A LEU* 1.4 75.3 - - - +
378A GLY* 1.3 58.2 + - - +
379A TRP* 3.3 40.9 + - + -
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 5.6 1.6 - - - -
375A GLU* 3.0 17.3 + - - -
376A LEU 3.3 0.8 + - - -
377A LEU* 1.3 78.6 - - - +
379A TRP* 1.3 64.6 + - - +
380A THR 3.6 3.1 - - - -
381A GLU* 3.9 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