Contacts of the helix formed by residues 317 - 330 (chain A) in PDB entry 1W57
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 PHE 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A VAL* 4.7 8.7 - - + -
233A GLN 3.6 24.7 - - - -
234A ILE* 3.1 51.6 - - + -
312A PRO* 6.3 0.7 - - + -
313A LYS 4.2 17.3 - - - -
314A LEU* 3.0 15.2 + - - +
316A ASP* 1.3 91.5 - - + +
318A LYS* 1.3 60.1 + - - +
319A GLN 3.5 2.0 - - - -
320A ALA* 3.2 11.9 + - + +
321A MET* 2.9 32.4 + - + +
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Residues in contact with LYS 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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314A LEU* 3.3 9.6 + - + +
315A LYS* 3.4 43.8 + - - +
316A ASP 3.6 0.2 - - - -
317A PHE* 1.3 74.5 - - - +
319A GLN* 1.3 76.8 + - - +
321A MET* 3.6 18.0 - - + +
322A GLN* 3.1 32.1 + - - +
338A VAL* 3.1 29.6 - - + +
339A LYS* 4.7 2.3 - - - +
340A ALA* 4.4 23.5 + - + +
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Residues in contact with GLN 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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315A LYS 5.0 1.8 + - - -
316A ASP 5.0 2.5 + - - +
317A PHE 3.5 0.4 - - - -
318A LYS* 1.3 87.2 - - - +
320A ALA* 1.3 57.7 + - - +
322A GLN* 3.8 22.1 - - - +
323A SER* 3.0 31.2 + - - -
333A GLU* 5.1 2.2 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 3.4 30.6 - - + +
316A ASP 5.3 2.6 + - - +
317A PHE* 3.2 16.7 + - + +
318A LYS 3.2 0.8 - - - -
319A GLN* 1.3 77.8 - - - +
321A MET* 1.3 59.0 + - - +
323A SER* 3.8 5.4 - - - -
324A ASN* 3.0 21.7 + - - +
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Residues in contact with MET 321 (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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229A LEU* 3.4 40.6 - - - +
230A ALA* 3.9 8.7 - - + +
232A VAL* 3.8 12.6 - - + -
234A ILE* 4.2 10.5 - - + -
249A LEU* 4.2 9.6 - - - -
307A VAL* 5.3 1.1 - - + -
314A LEU* 4.2 19.1 - - + +
317A PHE* 2.9 25.3 + - + +
318A LYS* 3.6 27.6 - - + +
320A ALA* 1.3 73.6 - - - +
322A GLN* 1.3 67.0 + - - +
324A ASN* 3.1 3.8 + - - +
325A ILE* 3.0 29.0 + - - +
338A VAL* 3.7 21.8 - - + -
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 3.1 21.8 + - - +
319A GLN* 3.8 24.8 - - - +
321A MET* 1.3 76.1 - - - +
323A SER* 1.3 62.8 + - - +
325A ILE* 3.3 2.1 + - - +
326A ALA* 3.0 25.0 + - - +
333A GLU* 4.9 9.4 - - + +
336A ILE* 3.3 41.5 - - + +
337A ASN* 3.7 10.1 + - - +
338A VAL* 3.1 40.5 + - + +
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Residues in contact with SER 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 GLN 3.0 21.7 + - - -
320A ALA* 3.8 7.6 - - - -
322A GLN* 1.3 77.1 - - - +
324A ASN* 1.3 59.7 + - - +
326A ALA* 3.6 3.5 - - - +
327A HIS* 3.2 22.2 + - - +
333A GLU* 3.6 30.7 + - - +
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Residues in contact with ASN 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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230A ALA 2.8 27.2 + - - +
231A GLY* 3.2 20.0 + - - -
232A VAL* 4.0 4.5 - - + -
283A MET* 4.2 9.2 - - - +
320A ALA 3.0 18.4 + - - +
321A MET 3.1 2.8 + - - +
323A SER* 1.3 73.0 - - - +
325A ILE* 1.3 57.4 + - - +
327A HIS* 3.2 14.0 + - - +
328A THR* 2.7 43.2 + - - -
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Residues in contact with ILE 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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230A ALA* 3.8 22.7 - - + -
249A LEU* 4.0 5.2 - - + -
253A LEU* 3.9 14.1 - - + -
283A MET* 4.0 13.2 - - + -
286A LEU* 5.1 0.9 - - + -
303A ILE* 4.0 1.1 - - + -
305A ILE* 3.8 23.6 - - + -
321A MET 3.0 15.6 + - - +
322A GLN 3.7 4.5 - - - +
324A ASN* 1.3 71.8 - - - +
326A ALA* 1.3 68.1 + - - +
327A HIS 3.0 0.9 + - - -
328A THR* 3.0 2.3 + - - -
329A LEU* 2.8 47.9 + - + +
336A ILE* 3.8 32.5 - - + -
338A VAL* 4.2 7.2 - - + -
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Residues in contact with ALA 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 GLN 3.0 17.2 + - - +
323A SER 3.6 6.7 - - - +
325A ILE* 1.3 76.6 - - - +
327A HIS* 1.3 58.0 + - - +
330A ASP* 3.0 22.7 + - - -
331A LEU* 3.0 33.0 + - - +
333A GLU* 3.9 25.8 - - + +
336A ILE* 4.1 11.3 - - + +
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Residues in contact with HIS 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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287A LYS* 5.3 1.6 + - - -
323A SER 3.2 11.0 + - - +
324A ASN* 3.6 17.8 + - - +
325A ILE 3.1 0.8 - - - -
326A ALA* 1.3 76.5 - - - +
328A THR* 1.3 70.3 + - - +
330A ASP* 3.3 12.6 + - - +
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Residues in contact with THR 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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283A MET* 3.2 55.4 - - + +
284A GLU* 5.3 0.4 - - - -
286A LEU* 4.7 2.9 - - + -
287A LYS* 3.3 46.7 + - + +
324A ASN* 2.7 27.3 + - - -
325A ILE* 3.0 3.6 + - - -
327A HIS* 1.3 82.7 + - - +
329A LEU* 1.3 61.5 + - - +
330A ASP* 3.2 2.3 + - - +
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Residues in contact with LEU 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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253A LEU* 4.3 4.5 - - + -
257A ILE* 3.8 16.2 - - + -
286A LEU* 3.9 28.5 - - + +
287A LYS* 4.3 7.6 - - - -
290A TYR* 3.3 57.9 - - + -
294A ARG* 5.4 1.7 + - - -
300A LEU* 3.8 4.9 - - + -
303A ILE* 3.7 29.8 - - + -
325A ILE* 2.8 28.4 + - + +
328A THR* 1.3 72.8 - - - +
330A ASP* 1.3 70.8 + - - +
331A LEU* 3.5 13.3 - - + +
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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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294A ARG* 5.2 15.1 + - - +
326A ALA 3.0 11.8 + - - -
327A HIS* 3.3 7.5 + - - +
328A THR 3.2 5.0 - - - +
329A LEU* 1.3 81.8 - - - +
331A LEU* 1.3 59.8 + - - +
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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