Contacts of the helix formed by residues 359 - 374 (chain A) in PDB entry 4OG2
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 GLN 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LYS 3.6 6.1 + - - +
358A ILE* 1.3 76.7 - - - +
360A LEU* 1.3 67.0 + - - +
361A PRO* 3.4 10.1 - - + -
362A GLU* 3.2 11.0 + - + +
363A LEU 2.9 18.4 + - - -
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Residues in contact with LEU 360 (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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122A LYS* 3.8 42.8 - - + +
123A VAL 4.0 3.1 - - - +
124A VAL* 4.3 15.3 - - + -
358A ILE 3.7 1.5 + - - -
359A GLN* 1.3 71.7 - - - +
361A PRO* 1.3 71.2 - - + +
363A LEU* 3.2 10.7 + - + -
364A ARG* 2.9 68.1 + - + +
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Residues in contact with PRO 361 (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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146A LYS* 4.8 1.6 - - - +
359A GLN* 3.5 10.8 - - + -
360A LEU* 1.3 94.5 - - + +
362A GLU* 1.3 60.2 + - - +
364A ARG* 3.5 14.9 + - - +
365A THR* 3.2 24.4 + - - -
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Residues in contact with GLU 362 (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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353A ASN* 5.4 5.5 + - - -
358A ILE* 3.7 20.0 - - + +
359A GLN* 3.2 13.8 + - + +
361A PRO* 1.3 77.6 - - - +
363A LEU* 1.3 60.7 + - - +
365A THR* 3.3 6.7 + - + +
366A GLU* 2.8 46.0 + - + +
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Residues in contact with LEU 363 (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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55A ILE* 5.8 2.5 - - + -
124A VAL* 3.7 29.8 - - + -
346A LEU* 4.6 9.2 - - + -
349A LEU* 3.6 24.0 - - + -
355A VAL* 3.8 35.2 - - + +
358A ILE* 3.3 21.0 - - + +
359A GLN 2.9 16.5 + - - +
360A LEU* 3.5 11.9 - - + +
362A GLU* 1.3 75.7 - - - +
364A ARG* 1.3 58.0 + - - +
366A GLU* 4.0 2.0 - - - +
367A LEU* 2.8 34.1 + - + +
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Residues in contact with ARG 364 (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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118A ILE* 3.0 40.6 + - - +
123A VAL* 2.8 33.5 + - - +
124A VAL* 3.5 23.8 - - - +
145A ALA 5.1 3.0 + - - -
146A LYS 3.4 15.3 - - - +
147A VAL* 3.7 27.7 - - - +
148A PRO* 3.6 11.5 - - + +
360A LEU* 2.9 48.1 + - + +
361A PRO* 3.6 10.0 - - - +
363A LEU* 1.3 77.6 - - - +
365A THR* 1.3 62.4 + - - +
367A LEU* 3.7 1.2 - - - +
368A ASN* 3.0 24.9 + - - +
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Residues in contact with THR 365 (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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146A LYS* 4.1 11.8 - - - +
165A TYR* 2.8 30.5 + - - +
361A PRO 3.2 15.6 + - - -
362A GLU* 3.3 6.9 + - - -
364A ARG* 1.3 77.0 - - - +
366A GLU* 1.3 68.3 + - + +
368A ASN* 3.4 4.0 + - - +
369A LYS* 3.0 29.4 + - + +
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Residues in contact with GLU 366 (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 LEU* 4.0 28.6 - - + +
353A ASN* 4.9 11.0 + - - +
358A ILE* 5.3 2.0 - - + -
362A GLU* 2.8 40.3 + - + +
363A LEU* 4.0 3.1 - - - +
365A THR* 1.3 78.7 - - + +
367A LEU* 1.3 60.6 + - - +
369A LYS* 3.4 27.6 + - - +
370A GLN* 2.9 30.1 + - - +
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Residues in contact with LEU 367 (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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124A VAL* 3.6 44.4 - - + +
148A PRO* 4.4 1.8 - - + -
342A TYR* 3.9 28.3 - - + +
345A SER* 3.8 28.9 - - - +
346A LEU* 3.8 27.8 - - + +
349A LEU* 3.9 11.3 - - + +
363A LEU* 2.8 19.9 + - + +
364A ARG 3.7 3.6 - - - +
366A GLU* 1.3 74.3 - - - +
368A ASN* 1.3 59.6 + - - +
370A GLN* 3.2 1.4 + - - +
371A LEU* 2.9 29.0 + - + +
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Residues in contact with ASN 368 (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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148A PRO* 3.6 14.5 - - + +
164A ASP* 2.9 24.8 + - - +
165A TYR* 3.4 48.2 - - + +
167A ALA* 6.1 0.9 - - - +
364A ARG 3.0 17.4 + - - +
365A THR 3.6 4.9 + - - +
367A LEU* 1.3 78.9 - - - +
369A LYS* 1.3 64.4 + - - +
371A LEU* 3.4 16.0 + - - +
372A LEU* 3.3 30.8 + - - +
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Residues in contact with LYS 369 (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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365A THR* 3.0 19.9 + - + +
366A GLU* 3.7 28.0 + - - +
368A ASN* 1.3 80.2 - - - +
370A GLN* 1.3 64.7 + - - +
372A LEU* 3.6 11.6 + - - +
373A THR* 3.4 23.3 + - + +
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Residues in contact with GLN 370 (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 SER* 3.4 31.8 + - - +
348A ALA* 3.5 22.5 - - - +
349A LEU* 4.1 11.2 + - + +
352A LYS* 2.8 34.9 + - - +
366A GLU 2.9 18.3 + - - +
367A LEU* 3.6 6.3 - - - +
369A LYS* 1.3 77.7 - - - +
371A LEU* 1.3 63.2 + - - +
373A THR* 2.8 35.8 + - - -
374A GLY* 3.5 8.2 + - - +
376A TYR* 4.3 0.3 + - - -
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Residues in contact with LEU 371 (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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148A PRO* 4.1 9.2 - - + -
149A VAL 5.9 0.2 - - - +
150A VAL* 4.1 9.2 - - + -
167A ALA* 4.2 20.0 - - + -
341A VAL* 4.0 9.9 - - + -
342A TYR* 3.8 30.5 - - + -
345A SER* 3.1 25.8 - - - +
367A LEU* 2.9 21.6 + - + +
368A ASN* 3.5 18.6 - - - +
370A GLN* 1.3 74.2 - - - +
372A LEU* 1.3 73.0 + - + +
373A THR 3.2 1.0 + - - -
374A GLY 3.2 2.6 + - - -
376A TYR* 2.7 17.6 + - - +
385A PHE* 3.3 29.6 - - + -
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Residues in contact with LEU 372 (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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164A ASP* 4.0 22.0 - - + +
166A VAL 5.6 0.7 - - - +
167A ALA* 4.3 13.5 - - + -
368A ASN* 3.3 23.9 + - - +
369A LYS* 3.8 8.5 - - - +
370A GLN 3.1 0.8 - - - -
371A LEU* 1.3 83.5 - - + +
373A THR* 1.3 59.6 + - + +
374A GLY 3.4 0.8 + - - -
385A PHE* 3.8 35.2 + - + +
386A THR 4.1 4.8 - - - +
387A PRO* 4.4 13.6 - - + +
388A ILE 4.7 0.7 - - - -
389A GLY* 3.6 34.8 - - - +
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Residues in contact with THR 373 (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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352A LYS* 5.6 0.7 + - - -
369A LYS* 3.4 20.4 - - + +
370A GLN* 2.8 30.2 + - - -
372A LEU* 1.3 78.8 - - + +
374A GLY* 1.3 64.2 + - - +
375A LYS* 3.3 19.2 + - - +
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Residues in contact with GLY 374 (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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370A GLN* 3.5 7.7 + - - -
371A LEU 3.2 6.9 + - - +
372A LEU 3.4 0.2 - - - -
373A THR* 1.3 85.1 + - - +
375A LYS* 1.3 60.2 + - - +
376A TYR* 3.3 31.4 - - - -
384A SER* 3.5 19.1 - - - -
385A PHE 4.3 2.6 + - - -
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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