Contacts of the helix formed by residues 347 - 357 (chain A) in PDB entry 1OH6
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 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 4.6 2.1 - - - +
301A PRO* 3.9 20.5 - - + +
302A MET* 3.8 6.6 - - - +
305A ARG* 2.3 39.7 + - - -
345A VAL 3.7 0.8 + - - -
346A GLY* 1.3 68.6 - - - -
348A LEU* 1.3 61.9 + - - +
349A GLU* 3.6 4.7 - - - +
350A ARG* 3.2 30.7 + - + +
351A ILE* 3.4 27.0 + - - +
354A ARG* 5.7 0.6 + - - -
367A ARG* 5.2 11.9 - - - +
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Residues in contact with LEU 348 (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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302A MET* 4.0 13.6 - - + -
345A VAL* 4.0 10.9 + - + +
346A GLY 3.4 5.1 + - - -
347A ASP* 1.3 72.6 - - - +
349A GLU* 1.3 65.6 + - - +
351A ILE* 3.7 10.3 - - + +
352A LEU* 3.1 59.7 + - + +
368A MET* 3.8 28.9 - - + -
371A ALA* 4.7 11.7 - - + -
372A PHE* 5.1 11.4 - - + -
375A LEU* 6.4 0.7 - - + -
542A LEU* 4.7 2.7 - - + +
545A SER* 4.4 8.3 - - - +
546A ALA* 4.0 18.6 - - + +
549A LEU* 4.3 15.3 - - + -
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Residues in contact with GLU 349 (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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149A ASP* 3.8 8.1 - - - +
151A SER 3.8 5.4 - - - +
152A SER* 3.4 34.7 - - - -
154A ARG* 4.2 8.9 + - - -
302A MET* 3.6 29.5 - - - +
305A ARG* 2.8 23.8 + - - -
306A MET* 5.8 1.0 - - - +
309A ARG* 4.8 8.2 + - - -
347A ASP* 3.1 8.5 - - - +
348A LEU* 1.3 81.3 - - - +
350A ARG* 1.3 63.2 + - - +
352A LEU* 3.3 5.3 + - - +
353A ALA* 3.2 14.6 + - - +
546A ALA* 4.0 13.9 - - + +
547A SER* 5.9 1.4 - - - -
550A ALA* 5.0 5.0 - - - +
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Residues in contact with ARG 350 (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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120A SER 5.0 1.3 - - - +
125A LEU* 3.8 32.8 - - + +
126A GLN 2.8 27.7 + - - -
127A GLU* 3.6 8.7 + - - +
129A GLN 3.1 22.2 + - - -
130A ASP* 3.9 8.3 + - - +
131A ASN 4.2 5.3 - - - +
149A ASP* 5.3 4.0 + - - -
151A SER* 3.4 34.0 + - - +
305A ARG* 3.3 30.6 - - - +
347A ASP* 3.2 30.3 + - - +
349A GLU* 1.3 78.0 + - - +
351A ILE* 1.3 64.6 + - - +
353A ALA* 3.2 5.8 + - - +
354A ARG* 3.1 42.2 + - - +
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Residues in contact with ILE 351 (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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345A VAL 5.5 2.7 - - - +
347A ASP 3.4 21.3 + - - +
348A LEU* 3.7 12.1 - - + +
349A GLU 3.3 0.2 - - - -
350A ARG* 1.3 77.4 - - - +
352A LEU* 1.3 57.7 + - - +
354A ARG* 3.1 27.7 + - - +
355A LEU* 2.8 24.9 + - - +
360A ALA* 4.6 1.9 - - + +
364A ASP* 3.5 29.8 - - + +
367A ARG* 3.9 42.0 - - + +
368A MET* 4.0 29.8 - - + +
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Residues in contact with LEU 352 (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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254A HIS* 5.2 0.6 - - - +
348A LEU* 3.1 42.8 + - + +
349A GLU* 3.7 4.9 - - - +
351A ILE* 1.3 72.8 - - - +
353A ALA* 1.3 60.5 + - - +
355A LEU* 3.4 14.0 - - + +
356A ALA* 2.9 28.4 + - - +
368A MET* 4.1 21.3 - - + -
539A LEU* 3.9 14.0 - - + +
542A LEU* 3.3 54.3 - - + +
543A GLN* 3.8 10.5 - - + +
546A ALA* 4.0 8.1 - - + -
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Residues in contact with ALA 353 (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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120A SER* 5.4 0.9 - - - -
150A ILE 4.2 4.9 - - - +
151A SER* 3.3 44.2 - - - +
152A SER* 4.0 2.7 - - - +
254A HIS* 4.4 8.3 - - + -
349A GLU 3.2 5.4 + - - +
350A ARG 3.2 11.6 + - - +
351A ILE 3.1 0.2 - - - -
352A LEU* 1.3 77.3 - - - +
354A ARG* 1.3 57.8 + - + +
356A ALA* 3.1 7.6 + - - +
357A LEU* 2.9 36.6 + - + +
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Residues in contact with ARG 354 (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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120A SER* 3.2 29.0 + - - +
121A ASP* 4.6 8.7 - - - -
122A GLU* 3.2 43.9 - - - +
125A LEU* 5.2 0.4 - - - +
347A ASP* 5.7 0.2 + - - -
350A ARG* 3.1 30.6 + - - +
351A ILE* 3.1 29.0 + - - +
353A ALA* 1.3 76.4 - - - +
355A LEU* 1.3 65.8 + - - +
357A LEU* 3.2 6.9 + - - +
358A ARG 2.9 3.8 + - - -
359A THR* 2.9 39.1 + - + -
360A ALA* 3.3 18.3 + - + +
361A ARG* 6.0 1.6 - - - +
364A ASP* 2.8 44.4 + - - -
367A ARG* 4.4 4.0 - - - +
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Residues in contact with LEU 355 (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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351A ILE 2.8 13.5 + - - +
352A LEU* 3.4 21.5 - - + +
353A ALA 3.2 0.2 - - - -
354A ARG* 1.3 76.3 - - - +
356A ALA* 1.3 62.2 + - - +
358A ARG* 3.1 13.6 + - - +
360A ALA* 3.8 9.3 - - + +
365A LEU* 4.8 0.9 - - + -
368A MET* 4.0 23.6 - - + -
532A PHE* 3.6 29.1 - - + -
535A LEU* 4.0 35.0 - - + -
536A LEU* 3.6 29.9 - - + +
539A LEU* 4.4 7.2 - - + -
542A LEU* 4.4 11.2 - - + -
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Residues in contact with ALA 356 (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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251A THR* 4.3 3.5 + - - +
253A PRO* 3.7 20.6 - - + +
254A HIS* 3.5 37.7 - - + +
352A LEU 2.9 15.1 + - - +
353A ALA 3.1 8.9 + - - +
355A LEU* 1.3 76.1 - - - +
357A LEU* 1.3 61.0 + - - +
358A ARG* 3.5 6.1 + - - +
536A LEU* 4.0 13.2 - - - +
539A LEU* 3.7 12.3 - - + -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.5 33.9 - - - +
150A ILE* 4.5 13.0 - - + +
248A GLN* 4.0 21.5 - - + +
250A THR* 4.3 25.0 + - - +
251A THR 4.7 1.8 - - - +
252A LEU* 3.6 31.6 - - + -
254A HIS* 4.0 10.1 - - + -
353A ALA 2.9 22.6 + - - +
354A ARG* 3.2 5.8 + - - +
355A LEU 3.2 0.2 - - - -
356A ALA* 1.3 76.0 - - - +
358A ARG* 1.3 69.1 + - - +
359A THR* 3.4 16.3 + - - +
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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