Contacts of the helix formed by residues 359 - 374 (chain B) in PDB entry 4OTZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B LYS 4.0 5.3 + - - +
358B ILE* 1.3 77.3 - - - +
360B LEU* 1.3 63.6 + - - +
361B PRO* 3.4 9.8 - - + +
362B GLU* 3.2 10.4 + - + +
363B LEU 2.9 24.8 + - - -
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Residues in contact with LEU 360 (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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122B LYS* 3.7 42.0 - - + +
123B VAL 4.1 2.9 - - - +
124B VAL* 4.1 16.4 - - + -
358B ILE 3.7 1.8 + - - -
359B GLN* 1.3 72.9 - - - +
361B PRO* 1.3 72.5 - - + +
363B LEU* 3.2 9.5 + - + +
364B ARG* 2.9 69.6 + - + +
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Residues in contact with PRO 361 (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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146B LYS* 4.9 1.4 - - - +
359B GLN* 3.6 10.3 - - + +
360B LEU* 1.3 93.0 - - + +
362B GLU* 1.3 60.5 + - - +
364B ARG* 3.5 15.1 + - - +
365B THR* 3.2 26.2 + - - -
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Residues in contact with GLU 362 (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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358B ILE* 3.7 11.9 - - + -
359B GLN* 3.2 13.7 + - + +
361B PRO* 1.3 77.1 - - - +
363B LEU* 1.3 60.0 + - - +
365B THR* 3.2 11.0 + - - +
366B GLU* 2.7 63.5 + - - +
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Residues in contact with LEU 363 (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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55B ILE* 5.6 2.5 - - + -
124B VAL* 3.8 31.0 - - + -
346B LEU* 4.6 10.3 - - + -
349B LEU* 3.7 24.0 - - + -
355B VAL* 3.8 36.1 - - + +
358B ILE* 3.4 21.0 - - + +
359B GLN 2.9 16.9 + - - +
360B LEU* 3.2 11.4 + - + +
362B GLU* 1.3 76.3 - - - +
364B ARG* 1.3 57.4 + - - +
366B GLU* 3.7 2.0 - - - -
367B LEU* 2.8 34.0 + - + +
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Residues in contact with ARG 364 (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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118B ILE* 3.0 39.8 + - - +
123B VAL* 2.9 30.3 + - - +
124B VAL* 3.5 25.1 - - - +
145B ALA 4.8 4.0 + - - -
146B LYS 3.4 16.8 - - - +
147B VAL* 3.6 27.5 - - - +
148B PRO* 3.6 12.0 - - + +
360B LEU* 2.9 50.4 + - + +
361B PRO* 3.6 11.5 - - - +
363B LEU* 1.3 75.2 - - - +
365B THR* 1.3 59.1 + - - +
367B LEU* 3.7 1.6 - - - +
368B ASN* 3.0 28.6 + - - +
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Residues in contact with THR 365 (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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146B LYS* 4.3 11.3 - - - +
165B TYR* 2.8 31.5 + - - +
361B PRO 3.2 17.3 + - - -
362B GLU* 3.7 14.8 - - - +
364B ARG* 1.3 79.1 - - - +
366B GLU* 1.3 62.5 + - + +
368B ASN* 3.4 4.0 + - - +
369B LYS* 3.0 24.8 + - + +
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Residues in contact with GLU 366 (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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349B LEU* 3.3 34.4 - - + +
353B ASN* 3.4 23.8 + - - +
358B ILE* 3.7 8.4 - - - +
362B GLU* 2.7 52.2 + - - +
363B LEU* 3.9 1.8 - - - +
365B THR* 1.3 77.7 - - + +
367B LEU* 1.3 58.9 + - - +
369B LYS* 3.4 9.2 + - + +
370B GLN* 2.9 30.3 + - - +
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Residues in contact with LEU 367 (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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124B VAL* 3.6 44.0 - - + +
148B PRO* 4.4 1.6 - - + -
342B TYR* 3.8 28.3 - - + +
345B SER* 3.8 27.4 - - - +
346B LEU* 3.9 29.4 - - + +
349B LEU* 3.8 10.7 - - + +
363B LEU* 2.8 23.7 + - + +
364B ARG 3.7 4.0 - - - +
366B GLU* 1.3 70.9 - - - +
368B ASN* 1.3 61.4 + - - +
370B GLN* 3.3 1.6 + - + +
371B LEU* 2.9 29.0 + - + +
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Residues in contact with ASN 368 (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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148B PRO* 3.7 11.2 - - + +
164B ASP* 2.9 24.0 + - - +
165B TYR* 3.4 51.4 - - + +
167B ALA* 6.1 0.9 - - - +
364B ARG 3.0 17.7 + - - +
365B THR 3.6 5.1 + - - +
367B LEU* 1.3 79.1 - - - +
369B LYS* 1.3 65.0 + - - +
371B LEU* 3.5 16.2 + - - +
372B LEU* 3.4 30.0 + - - +
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Residues in contact with LYS 369 (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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365B THR* 3.0 19.4 + - + +
366B GLU* 3.7 8.7 - - + +
368B ASN* 1.3 81.0 - - - +
370B GLN* 1.3 63.1 + - - +
372B LEU* 3.5 11.2 + - - +
373B THR* 3.3 28.1 - - + +
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Residues in contact with GLN 370 (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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345B SER* 3.4 30.8 + - - +
348B ALA* 3.5 22.6 - - - +
349B LEU* 4.2 13.5 + - + +
352B LYS* 2.9 34.0 + - - +
366B GLU 2.9 17.9 + - - +
367B LEU* 3.7 6.5 - - - +
369B LYS* 1.3 77.8 - - - +
371B LEU* 1.3 64.3 + - - +
373B THR* 2.8 35.3 + - - -
374B GLY* 3.5 8.0 + - - +
376B TYR* 4.2 0.3 + - - -
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Residues in contact with LEU 371 (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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148B PRO* 4.2 7.9 - - + -
150B VAL* 4.1 15.0 - - + -
167B ALA* 4.2 16.8 - - + -
341B VAL* 4.0 7.0 - - + -
342B TYR* 3.8 30.1 - - + -
345B SER* 3.1 24.7 - - - +
367B LEU 2.9 19.5 + - - +
368B ASN* 3.5 20.4 - - - +
369B LYS 3.4 0.2 - - - -
370B GLN* 1.3 77.9 - - - +
372B LEU* 1.3 74.4 - - + +
373B THR 3.2 0.9 + - - -
374B GLY 3.2 3.3 + - - -
376B TYR* 2.7 16.5 + - - +
385B PHE* 3.3 28.1 - - + -
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Residues in contact with LEU 372 (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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164B ASP 4.2 19.3 - - - +
166B VAL 5.6 0.4 - - - +
167B ALA* 4.3 14.1 - - + -
368B ASN* 3.4 22.1 + - - +
369B LYS* 3.9 10.3 - - - +
370B GLN 3.2 1.0 - - - -
371B LEU* 1.3 82.6 - - + +
373B THR* 1.3 59.8 + - + +
374B GLY 3.7 0.2 + - - -
385B PHE* 3.7 32.0 + - + +
386B THR 4.1 11.5 - - - +
387B PRO* 4.2 16.5 - - + +
388B ILE 5.0 0.4 - - - -
389B GLY* 3.7 30.5 - - - +
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Residues in contact with THR 373 (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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352B LYS* 5.3 1.7 + - - -
369B LYS* 3.3 27.1 - - + +
370B GLN* 2.8 29.5 + - - -
372B LEU* 1.3 80.2 - - + +
374B GLY* 1.3 63.0 + - - +
375B LYS* 3.9 16.1 + - - +
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Residues in contact with GLY 374 (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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370B GLN* 3.5 7.2 + - - -
371B LEU 3.2 7.7 + - - +
372B LEU 3.4 0.2 - - - -
373B THR* 1.3 84.8 + - - +
375B LYS* 1.3 62.4 + - - +
376B TYR* 3.3 30.5 - - - -
384B SER* 3.5 19.6 - - - -
385B PHE 4.3 2.4 + - - -
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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