Contacts of the helix formed by residues 325 - 337 (chain A) in PDB entry 4OWW
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A MET* 4.8 1.6 - - + -
320A VAL* 3.9 9.2 - - + -
321A ARG 4.1 0.2 + - - -
322A PHE* 3.9 13.8 - - - -
323A GLY* 2.7 34.8 + - - +
324A GLN* 1.3 76.8 - - - +
326A LYS* 1.3 65.4 + - - +
327A ARG 3.5 1.3 - - - -
328A TYR* 3.5 8.3 + - - +
329A GLN* 3.1 51.9 + - + +
369A LEU* 3.6 41.1 - - + +
373A ALA* 5.1 3.2 + - - +
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Residues in contact with LYS 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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323A GLY 5.5 3.1 - - - +
324A GLN 3.3 3.4 - - - -
325A GLN* 1.3 82.8 - - + +
327A ARG* 1.3 65.3 + - + +
329A GLN* 3.4 10.0 + - - +
330A ASP* 2.9 63.1 + - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN 4.8 0.6 + - - -
326A LYS* 1.3 81.7 - - + +
328A TYR* 1.3 60.2 + - - +
330A ASP* 3.2 9.3 + - - +
331A TRP* 2.9 57.5 + - + +
24B LEU* 3.5 35.8 + - - +
25B GLU* 2.8 37.2 + - - +
42B LYS* 4.7 0.8 - - - +
102B TYR* 3.3 24.9 + - + +
104B GLU* 2.5 38.7 + - - +
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Residues in contact with TYR 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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315A PHE* 3.6 9.9 - + - -
316A MET* 4.1 12.8 - - + -
320A VAL* 3.7 29.0 - - + +
324A GLN* 3.6 26.2 - - + -
325A GLN* 3.7 6.1 - - - +
326A LYS 3.4 0.2 - - - -
327A ARG* 1.3 76.7 - - - +
329A GLN* 1.3 57.1 + - - +
331A TRP* 3.9 17.5 - + - -
332A PHE* 2.9 26.9 + - - +
98B PHE* 3.2 62.9 - + + -
100B MET 2.5 24.1 + - - -
101B VAL* 3.8 6.2 - - - -
102B TYR* 3.3 26.3 + + - -
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Residues in contact with GLN 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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316A MET* 3.7 15.4 - - + +
325A GLN* 3.1 44.7 + - - +
326A LYS* 3.6 10.1 - - - +
328A TYR* 1.3 77.8 - - - +
330A ASP* 1.3 55.7 + - - +
332A PHE 3.3 0.2 + - - -
333A GLN* 2.7 39.0 + - - +
369A LEU* 5.1 1.4 - - - +
373A ALA 4.5 6.3 + - - -
374A ILE* 5.0 2.0 - - - +
377A TRP* 3.3 70.7 - - + +
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Residues in contact with ASP 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 LYS* 2.9 49.2 + - - +
327A ARG* 3.7 8.6 - - - +
329A GLN* 1.3 77.4 - - - +
331A TRP* 1.3 63.1 + - + +
333A GLN* 3.8 12.4 - - - +
334A ARG* 2.9 50.9 + - - +
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Residues in contact with TRP 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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312A LYS* 6.2 0.4 - - - -
327A ARG* 2.9 45.9 + - + +
328A TYR* 3.7 30.3 - + - +
330A ASP* 1.3 80.9 - - + +
332A PHE* 1.3 61.2 + - - +
334A ARG* 3.4 14.1 + - - +
335A GLN* 3.1 25.5 + - - +
22B ILE* 3.6 33.0 - - + -
23B VAL 3.5 20.0 - - - -
24B LEU* 4.0 17.4 + - + -
64B PRO* 3.5 29.5 - - + +
65B GLY* 3.6 13.2 - - - -
98B PHE* 3.9 23.8 - + + -
102B TYR* 4.5 3.1 - + - -
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Residues in contact with PHE 332 (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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309A MET* 3.8 28.0 - - + -
312A LYS* 4.0 22.2 - - + -
313A LEU* 4.1 12.3 - - + -
316A MET* 4.9 6.7 - - - -
328A TYR 2.9 19.4 + - - +
329A GLN 3.6 3.6 - - - +
331A TRP* 1.3 76.0 - - - +
333A GLN* 1.3 57.7 + - - +
335A GLN* 3.2 2.1 + - - -
336A TYR* 3.0 61.5 + + + +
337A LEU* 4.0 8.5 - - + -
345A LEU* 5.4 0.2 - - + -
349A LEU* 3.6 41.3 - - + -
377A TRP* 3.7 24.2 - + + -
98B PHE* 4.0 8.2 - + + -
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Residues in contact with GLN 333 (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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329A GLN 2.7 19.5 + - - +
330A ASP* 3.8 13.5 - - - +
332A PHE* 1.3 74.4 - - - +
334A ARG* 1.3 57.6 + - - +
337A LEU* 2.7 56.8 + - + +
338A SER* 2.8 13.0 + - - +
346A ARG* 4.9 1.0 - - - +
377A TRP* 3.6 19.8 + - + -
381A THR* 3.8 26.7 - - - +
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Residues in contact with ARG 334 (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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330A ASP* 2.9 38.5 + - - +
331A TRP* 3.8 14.1 - - - +
333A GLN* 1.3 78.1 - - - +
335A GLN* 1.3 58.9 + - - +
338A SER* 3.3 18.6 + - - +
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Residues in contact with GLN 335 (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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135A LEU* 4.6 10.3 - - - +
308A ASP* 3.5 6.3 + - - -
312A LYS* 2.4 30.0 + - - +
331A TRP 3.1 15.6 + - - +
332A PHE* 3.9 3.3 - - - +
333A GLN 3.2 0.2 - - - -
334A ARG* 1.3 80.4 - - - +
336A TYR* 1.3 92.9 + - + +
337A LEU 3.9 0.2 - - - -
338A SER 5.5 0.2 - - - -
97B GLU* 4.2 6.1 + - - +
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Residues in contact with TYR 336 (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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135A LEU* 4.6 3.8 - - - +
306A THR* 4.0 4.3 + - + -
308A ASP* 2.2 44.1 + - - +
309A MET* 3.6 46.6 + - + -
312A LYS* 4.5 4.7 - - + -
332A PHE* 3.0 42.7 + + + +
335A GLN* 1.3 109.0 + - + +
337A LEU* 1.3 63.8 + - - +
338A SER 3.8 2.2 - - - -
339A THR* 6.4 0.4 - - - -
342A SER* 3.1 20.1 - - - -
345A LEU* 3.7 19.3 - - + +
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Residues in contact with LEU 337 (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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332A PHE* 4.0 23.3 - - + -
333A GLN* 2.7 39.7 + - + +
336A TYR* 1.3 84.2 - - - +
338A SER* 1.3 55.9 + - - +
339A THR 4.7 0.3 - - - +
342A SER* 3.2 12.6 + - - +
345A LEU* 4.1 16.6 - - + -
346A ARG* 2.9 52.4 + - - +
349A LEU* 4.3 7.6 - - + -
377A TRP* 4.1 12.1 - - + -
378A LEU* 4.1 22.2 - - + -
381A THR* 4.4 5.6 - - + +
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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