Contacts of the helix formed by residues 349 - 358 (chain A) in PDB entry 1O94
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 ASN 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA 3.0 23.2 + - - -
270A PRO* 3.9 11.4 - - + +
322A ARG* 2.7 36.6 + - - +
347A GLY 4.5 3.1 - - - -
348A CYS* 1.3 79.4 - - - +
350A VAL* 1.3 60.2 + - - +
351A CYS* 3.2 5.6 - - - +
352A ILE* 3.4 19.3 + - + +
353A SER* 3.0 25.6 + - - -
571A THR* 3.0 32.3 + - - +
572A LEU* 4.1 4.0 - - - +
1732A SF4 3.2 10.9 - - - -
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Residues in contact with VAL 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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348A CYS* 3.2 11.1 - - + +
349A ASN* 1.3 74.3 - - - +
351A CYS* 1.3 64.1 - - - +
353A SER* 2.5 29.6 + - - +
354A ARG* 3.4 9.1 + - + +
363A ILE* 3.7 32.0 - - + +
365A THR* 3.6 20.0 - - - +
539A TYR* 3.7 26.0 - - + +
567A TYR* 4.7 3.4 - - + +
571A THR* 4.9 0.9 - - + -
680A LEU* 4.1 18.2 - - + -
682A ALA* 4.1 11.9 - - + +
1732A SF4 4.1 1.1 - - - -
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Residues in contact with CYS 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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322A ARG* 4.0 13.9 - - - -
325A ILE* 4.4 4.7 - - + -
349A ASN* 4.3 2.2 - - - -
350A VAL* 1.3 77.2 - - - +
352A ILE* 1.3 71.8 + - - +
354A ARG* 3.7 15.1 + - - +
355A TRP* 3.7 3.6 + - - +
362A MET* 3.8 28.7 - - + +
363A ILE 3.2 20.8 + - - +
1730A FMN 4.0 15.4 - - + +
1732A SF4 2.3 49.7 - - - -
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Residues in contact with ILE 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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264A TRP* 3.6 29.6 - - + -
268A ALA* 3.4 32.3 - - + -
322A ARG* 4.4 0.4 - - - -
349A ASN* 3.4 27.8 + - + +
350A VAL 3.4 0.2 - - - -
351A CYS* 1.3 81.0 - - - +
353A SER* 1.4 56.0 - - - +
355A TRP* 2.9 8.0 + - + +
356A GLU* 2.9 27.0 + - + +
570A PHE 3.5 15.7 - - - +
572A LEU* 3.8 13.2 - - + -
1730A FMN 3.2 39.3 - - + -
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Residues in contact with SER 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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349A ASN 3.0 13.6 + - - -
350A VAL* 2.5 28.6 + - - +
352A ILE* 1.4 74.6 - - - +
354A ARG* 1.3 62.0 + - - +
356A GLU* 3.4 1.7 + - - +
357A ILE* 3.0 31.2 + - - +
567A TYR* 2.8 35.5 + - - -
570A PHE* 3.3 30.0 + - - +
571A THR* 4.1 1.3 - - - -
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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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350A VAL 3.4 10.5 + - - +
351A CYS 3.7 8.7 - - - +
353A SER* 1.3 82.6 + - - +
355A TRP* 1.3 62.8 + - - +
357A ILE* 3.3 16.9 + - - +
360A PRO* 3.3 36.8 - - - +
361A PRO* 3.0 40.5 + - - +
362A MET* 4.1 1.1 - - - -
363A ILE* 3.7 44.6 - - + +
567A TYR* 4.6 7.4 + - - -
680A LEU* 5.7 2.4 - - - +
683A ASP* 4.4 10.5 + - - -
112B PRO 5.8 0.2 + - - -
113B ASN 4.9 1.8 + - - -
114B MET* 2.7 51.3 + - - +
117B ARG* 5.2 3.0 - - - +
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Residues in contact with TRP 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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30A CYS* 3.5 38.4 - - + -
31A ILE 6.2 0.7 - - - -
32A GLY* 5.1 9.4 - - - +
60A TYR* 3.0 42.6 + + - -
69A ASP* 3.7 2.9 - - - -
72A ARG* 3.5 32.3 - - - +
73A LEU* 3.4 20.7 + - + -
130A PHE* 5.0 5.6 - + - -
174A TYR* 4.8 10.1 - - - -
261A ILE* 6.0 1.8 - - + -
264A TRP* 3.7 26.9 - + - -
351A CYS 3.7 3.6 + - - +
352A ILE 2.9 12.9 + - - +
354A ARG* 1.3 73.8 - - - +
356A GLU* 1.3 99.7 + - + +
358A GLY* 2.9 22.2 + - - -
359A GLY 4.3 2.4 + - - +
360A PRO 4.6 5.1 + - - -
362A MET* 5.7 0.6 - - - +
1730A FMN 5.8 3.4 - + - -
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Residues in contact with GLU 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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71A HIS* 4.2 8.7 - - - -
72A ARG* 4.4 8.4 + - - +
130A PHE* 4.2 21.9 - - - -
264A TRP* 2.8 30.0 + - - -
352A ILE* 2.9 14.2 + - + +
353A SER 3.7 5.4 - - - +
355A TRP* 1.3 96.7 - - + +
357A ILE* 1.3 62.0 + - - +
358A GLY* 3.3 1.6 + - - -
569A HIS 4.9 3.5 - - - +
570A PHE* 3.5 42.0 - - + +
572A LEU* 3.7 14.3 - - + +
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Residues in contact with ILE 357 (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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71A HIS* 3.3 16.3 + - - -
353A SER 3.0 24.8 + - - +
354A ARG* 3.7 10.8 - - - +
355A TRP 3.2 0.6 - - - -
356A GLU* 1.3 75.2 - - - +
358A GLY* 1.4 60.0 + - - +
360A PRO* 4.2 1.8 - - + -
567A TYR* 4.0 28.7 - - + +
570A PHE* 3.8 30.5 - - + -
71B HIS* 3.5 46.4 + - + +
114B MET* 4.0 25.8 - - + -
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Residues in contact with GLY 358 (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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71A HIS* 3.3 27.4 - - - -
72A ARG* 4.0 5.8 - - - -
354A ARG 3.5 2.4 + - - -
355A TRP 2.9 15.1 + - - -
357A ILE* 1.4 82.7 - - - +
359A GLY* 1.3 57.8 + - - +
360A PRO* 3.3 7.4 - - - +
71B HIS* 3.5 8.8 - - - +
358B GLY 3.4 18.7 - - - +
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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