Contacts of the helix formed by residues 317 - 331 (chain A) in PDB entry 1OH7
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ASP* 4.6 0.4 + - - +
315A VAL* 3.4 18.5 - - + +
316A ARG* 1.3 75.5 - - - +
318A THR* 1.3 67.7 + - - +
319A ARG* 3.2 19.2 + - - +
320A VAL* 3.3 26.7 + - + +
321A LEU* 3.1 23.9 + - - +
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Residues in contact with THR 318 (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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316A ARG 3.2 7.5 + - - -
317A ASP* 1.3 70.6 + - - +
319A ARG* 1.3 64.7 + - - +
321A LEU* 3.1 10.9 + - + +
322A LEU* 2.9 39.4 + - + +
572A PHE* 4.3 31.0 - - + -
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Residues in contact with ARG 319 (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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317A ASP* 3.2 13.6 + - - +
318A THR* 1.3 78.9 - - - +
320A VAL* 1.3 64.7 + - + +
322A LEU* 3.2 8.5 + - - +
323A GLU* 2.9 39.8 + - - +
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Residues in contact with VAL 320 (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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315A VAL* 4.7 12.1 - - + -
317A ASP* 3.3 32.8 + - + +
319A ARG* 1.3 79.8 - - + +
321A LEU* 1.3 62.8 + - + +
323A GLU* 3.4 13.5 + - - +
324A ARG* 3.1 57.7 + - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 4.0 13.2 - - + +
316A ARG 4.2 1.8 - - - +
317A ASP 3.1 26.7 + - - +
318A THR* 3.5 10.3 - - + +
319A ARG 3.1 0.4 + - - -
320A VAL* 1.3 75.1 - - + +
322A LEU* 1.3 65.4 + - - +
324A ARG* 3.2 6.9 + - - +
325A GLN* 3.0 29.0 + - - +
572A PHE* 3.8 23.3 - - + -
634A ALA 3.8 1.8 - - - +
635A TYR* 3.5 64.2 - - + +
636A ILE* 4.0 2.7 - - - -
637A GLY* 3.5 17.7 - - - +
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Residues in contact with LEU 322 (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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318A THR* 2.9 32.9 + - + +
319A ARG* 3.6 6.7 - - - +
321A LEU* 1.3 75.1 - - - +
323A GLU* 1.3 62.7 + - - +
325A GLN* 3.4 21.2 + - - +
326A GLN* 2.9 42.9 + - - +
572A PHE* 4.1 19.3 - - + -
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Residues in contact with GLU 323 (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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319A ARG* 2.9 29.2 + - - +
320A VAL* 3.4 19.1 - - - +
322A LEU* 1.3 77.4 - - - +
324A ARG* 1.3 56.8 + - + +
326A GLN* 3.3 14.8 + - - +
327A THR* 2.8 32.0 + - - -
389A PRO* 3.3 32.1 - - + +
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Residues in contact with ARG 324 (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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310A TRP* 3.4 51.3 - - + +
315A VAL* 3.6 27.2 - - - +
320A VAL* 3.1 34.6 + - + +
321A LEU* 3.2 9.0 + - - +
323A GLU* 1.3 79.4 - - + +
325A GLN* 1.3 60.3 + - - +
327A THR* 3.2 8.9 + - - -
328A ILE* 3.1 34.9 + - + +
551A GLU* 5.8 2.5 + - - +
555A LEU* 4.0 18.2 - - + +
636A ILE* 2.9 36.5 + - - +
637A GLY* 4.1 9.2 - - - +
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Residues in contact with GLN 325 (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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321A LEU 3.0 17.5 + - - +
322A LEU* 3.5 24.0 - - - +
324A ARG* 1.3 74.1 - - - +
326A GLN* 1.3 64.2 + - - +
328A ILE* 3.5 0.8 + - - -
329A GLY 3.3 14.6 + - - -
569A CYS* 3.5 26.9 - - - -
570A PRO* 3.5 28.0 + - + +
572A PHE* 3.2 34.6 - - - -
634A ALA 4.6 3.0 + - - -
637A GLY* 3.3 20.6 + - - +
638A SER 5.1 0.2 + - - -
639A TYR* 3.4 20.5 + - + -
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Residues in contact with GLN 326 (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 LEU* 2.9 36.8 + - - +
323A GLU* 3.3 12.1 - - - +
324A ARG 3.1 0.2 - - - -
325A GLN* 1.3 75.1 - - + +
327A THR* 1.3 60.8 + - - +
329A GLY* 3.2 2.8 + - - -
330A ALA* 3.0 29.0 + - - +
387A SER* 4.5 4.2 + - - +
389A PRO* 3.7 25.8 - - + +
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Residues in contact with THR 327 (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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323A GLU 2.8 17.5 + - - -
324A ARG* 3.4 10.6 - - - -
326A GLN* 1.3 78.0 - - - +
328A ILE* 1.3 62.1 + - - +
330A ALA* 3.4 1.0 + - - +
331A LEU* 3.1 53.0 + - + +
387A SER* 4.1 7.9 - - - -
389A PRO* 3.2 19.2 - - - +
390A VAL* 3.5 13.7 - - + -
393A LEU* 4.8 6.9 - - + +
552A LEU* 6.2 0.2 - - + -
555A LEU* 3.7 28.8 - - + +
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Residues in contact with ILE 328 (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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324A ARG* 3.1 20.8 + - + +
325A GLN* 3.7 4.9 - - - +
326A GLN 3.2 0.2 - - - -
327A THR* 1.3 79.9 - - - +
329A GLY* 1.3 58.7 + - - +
332A GLN* 3.2 21.4 + - - +
555A LEU* 3.8 31.0 - - + +
558A LEU* 4.0 17.9 - - + +
559A ALA* 3.3 29.4 - - - +
562A ALA* 4.6 0.4 - - + -
637A GLY 3.4 24.0 - - - +
638A SER* 3.9 13.7 - - - -
639A TYR* 3.5 30.5 - - + +
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Residues in contact with GLY 329 (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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325A GLN 3.3 5.2 + - - -
326A GLN* 3.2 5.8 + - - -
328A ILE* 1.3 79.1 - - - +
330A ALA* 1.3 61.6 + - - +
331A LEU 3.2 0.8 + - - -
332A GLN* 3.7 19.8 + - - +
639A TYR* 3.6 18.4 - - - -
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Residues in contact with ALA 330 (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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326A GLN 3.0 16.5 + - - +
327A THR* 3.7 5.6 - - - +
329A GLY* 1.3 78.0 - - - +
331A LEU* 1.3 58.3 + - - +
332A GLN 3.4 0.4 + - - -
333A ASP 4.8 0.3 + - - -
334A PHE* 3.3 23.9 - - - -
385A VAL* 3.8 13.7 - - + +
386A ASP 4.0 7.4 - - - +
387A SER* 3.6 28.0 - - - -
390A VAL* 4.5 0.2 - - + -
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Residues in contact with LEU 331 (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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327A THR* 3.1 41.4 + - + +
328A ILE 3.8 2.9 + - - +
329A GLY 3.2 0.2 - - - -
330A ALA* 1.3 77.5 - - - +
332A GLN* 1.3 66.8 + - - +
333A ASP 3.1 3.4 - - - -
334A PHE* 2.9 15.9 + - + -
335A THR* 3.3 13.6 + - + +
338A LEU* 3.7 27.4 - - + -
382A LEU* 4.1 9.6 - - + -
385A VAL* 3.9 23.3 - - + -
390A VAL* 4.0 11.4 - - + -
552A LEU* 4.9 5.6 - - + -
555A LEU* 4.6 2.2 - - + -
556A VAL* 4.1 27.4 - - + +
559A ALA* 4.4 7.4 - - + -
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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