Contacts of the helix formed by residues 313 - 328 (chain A) in PDB entry 4WPN
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 GLU 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A VAL 3.3 0.9 + - - -
312A GLU* 1.3 79.2 - - - +
314A SER* 1.3 63.2 + - - +
316A TYR* 3.2 21.6 + - + +
317A ASP* 4.6 4.2 + - - -
410A LYS* 4.2 27.4 + - + +
411A PHE 2.8 17.9 + - - +
412A LYS* 3.8 18.7 - - + +
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Residues in contact with SER 314 (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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280A ALA* 3.9 12.3 - - - +
312A GLU* 2.5 31.8 + - - -
313A GLU* 1.3 74.3 - - - +
315A ILE* 1.3 63.5 + - - +
317A ASP* 5.4 0.8 - - - +
318A GLU* 5.9 0.2 - - - +
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Residues in contact with ILE 315 (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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278A VAL* 4.0 12.1 - - + +
279A LEU 3.5 26.7 - - - +
280A ALA* 3.8 23.6 - - + +
282A ALA* 5.3 2.7 - - + +
284A LEU* 4.0 24.6 - - + +
311A VAL* 3.7 15.9 - - + -
312A GLU 3.4 12.1 - - - +
314A SER* 1.3 87.8 + - - +
316A TYR* 1.3 59.3 + - - +
317A ASP 3.4 2.0 - - - -
318A GLU* 3.5 8.7 + - + +
319A PHE* 3.0 30.5 + - - +
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Residues in contact with TYR 316 (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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311A VAL* 3.7 17.5 - - + +
312A GLU 3.1 8.5 + - - +
313A GLU* 3.2 20.6 + - + +
314A SER 3.6 0.2 - - - -
315A ILE* 1.3 77.3 - - - +
317A ASP* 1.3 74.8 + - - +
319A PHE* 3.2 2.4 + - - +
320A VAL* 2.9 45.9 + - + +
388A SER* 3.5 5.9 - - - -
389A ASN* 2.6 53.1 + - - -
408A ILE* 3.6 14.5 + - + -
409A MET 3.5 28.3 - - - -
410A LYS* 3.6 32.1 - - + -
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Residues in contact with ASP 317 (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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313A GLU 4.6 3.5 + - - +
314A SER 5.4 0.6 + - - -
315A ILE 3.4 0.4 - - - -
316A TYR* 1.3 95.0 - - - +
318A GLU* 1.3 57.2 + - - +
320A VAL* 3.2 7.1 + - - +
321A ARG* 3.0 29.2 + - - +
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Residues in contact with GLU 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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284A LEU* 3.5 15.7 - - + -
315A ILE* 3.5 12.5 + - + +
316A TYR 3.3 0.2 - - - -
317A ASP* 1.3 76.3 - - - +
319A PHE* 1.3 63.8 + - - +
321A ARG* 2.5 45.2 + - - +
322A ARG* 2.8 56.2 + - - +
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Residues in contact with PHE 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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278A VAL* 4.1 16.2 - - + -
284A LEU* 3.8 17.4 - - + +
287A ALA* 3.9 6.3 - - + -
288A VAL* 3.6 36.9 - - + +
291A ALA* 4.0 18.8 - - + -
309A ILE* 3.9 30.7 - - + -
311A VAL* 3.8 25.1 - - + -
315A ILE 3.0 19.0 + - - +
316A TYR 3.2 4.5 + - - +
318A GLU* 1.3 72.3 - - - +
320A VAL* 1.3 61.7 + - - +
322A ARG* 3.5 1.9 + - - +
323A SER* 2.8 51.0 + - - -
406A GLN* 5.2 0.4 - - - -
408A ILE* 4.2 15.5 - - + -
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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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316A TYR* 2.9 52.2 + - + +
317A ASP* 3.6 6.3 - - - +
319A PHE* 1.3 76.6 - - - +
321A ARG* 1.3 58.2 + - - +
323A SER* 3.2 5.8 + - - -
324A VAL* 2.9 35.7 + - + +
369A GLU* 4.0 20.9 - - + +
388A SER* 3.9 20.6 - - - -
408A ILE* 4.0 20.0 - - + -
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Residues in contact with ARG 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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317A ASP 3.0 16.1 + - - +
318A GLU* 2.5 41.6 + - - +
319A PHE 3.4 0.2 - - - -
320A VAL* 1.3 77.3 - - - +
322A ARG* 1.3 79.5 + - - +
324A VAL* 3.4 5.2 + - - +
325A GLU* 3.0 54.6 + - - +
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Residues in contact with ARG 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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284A LEU* 3.6 20.5 - - - +
285A ASP* 2.4 44.5 + - - +
288A VAL* 4.0 27.1 - - + +
318A GLU* 2.8 48.8 + - - +
319A PHE 4.0 0.2 - - - +
321A ARG* 1.3 92.5 - - - +
323A SER* 1.3 63.9 + - - +
325A GLU* 3.4 12.9 - - - +
326A ARG* 3.2 22.2 + - - +
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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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288A VAL* 4.0 14.6 + - - +
292A HIS* 4.6 5.3 + - - +
319A PHE* 2.8 46.4 + - - -
320A VAL 3.5 4.0 - - - -
322A ARG* 1.3 75.3 - - - +
324A VAL* 1.3 66.2 + - - +
326A ARG* 3.0 15.3 + - - +
327A ALA* 3.0 13.7 + - - +
386A VAL* 5.3 0.2 - - - -
406A GLN* 3.8 23.5 + - - +
408A ILE* 3.9 10.7 - - - +
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Residues in contact with VAL 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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320A VAL* 2.9 22.6 + - + +
321A ARG* 3.8 5.6 - - - +
323A SER* 1.3 74.5 - - - +
325A GLU* 1.3 62.5 + - - +
327A ALA* 3.3 7.6 + - - +
328A LYS* 3.1 46.5 + - + +
369A GLU* 3.3 52.0 - - + +
370A CYS* 4.3 3.1 - - - -
386A VAL* 3.9 13.9 - - + +
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Residues in contact with GLU 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 ARG* 3.0 41.7 + - - +
322A ARG* 3.4 16.4 - - - +
324A VAL* 1.3 78.7 - - - +
326A ARG* 1.3 61.8 + - - +
328A LYS* 3.5 12.7 + - - +
329A LYS* 3.5 32.1 - - - +
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Residues in contact with ARG 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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288A VAL* 5.1 5.4 - - + -
289A GLU* 3.4 30.2 + - - +
292A HIS* 3.4 37.2 + - + +
293A HIS* 3.4 27.1 + - - -
322A ARG 3.2 9.7 + - - +
323A SER* 3.0 11.2 + - - +
325A GLU* 1.3 79.3 - - - +
327A ALA* 1.3 61.6 + - - +
328A LYS 3.3 0.7 + - - -
329A LYS* 3.3 34.7 + - - +
330A TYR* 4.1 14.9 + - - -
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Residues in contact with ALA 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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292A HIS* 3.8 16.7 - - + -
296A PHE* 4.3 9.9 - - + -
323A SER 3.0 11.7 + - - +
324A VAL 3.3 7.8 + - - +
326A ARG* 1.3 76.0 - - - +
328A LYS* 1.3 58.8 + - - +
329A LYS 3.2 4.5 + - - -
330A TYR* 3.4 16.8 + - - -
370A CYS* 4.1 8.5 - - - -
384A PRO* 3.8 16.7 - - + +
386A VAL* 3.8 25.8 - - + -
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Residues in contact with LYS 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 VAL* 3.1 35.5 + - + +
325A GLU* 4.0 8.1 - - - +
326A ARG 3.2 1.0 - - - -
327A ALA* 1.3 77.6 - - - +
329A LYS* 1.3 61.1 + - - +
330A TYR 3.5 3.5 + - - +
369A GLU 5.2 3.4 + - - -
370A CYS* 4.1 21.8 - - + -
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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