Contacts of the helix formed by residues 283 - 297 (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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ALA* 1.3 67.8 - - - +
284A LEU* 1.3 65.1 + - - +
285A ASP* 3.4 8.1 + - - +
286A ASN* 3.2 33.2 + - + +
287A ALA* 3.0 23.0 + - - +
433A PHE* 5.6 0.3 - - - -
434A THR 5.7 0.2 - - - -
435A LYS* 3.4 25.9 + - - +
455A ASN* 5.6 3.1 + - - +
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Residues in contact with LEU 284 (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* 5.0 2.7 - - + -
282A ALA* 3.0 10.3 + - - +
283A ASP* 1.3 72.4 + - - +
285A ASP* 1.3 59.0 + - - +
287A ALA* 3.2 4.4 + - - +
288A VAL* 2.8 35.6 + - + +
315A ILE* 4.0 32.3 - - + +
318A GLU* 3.5 36.6 - - + -
319A PHE* 3.8 30.3 - - + -
322A ARG* 3.6 23.3 - - - +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 3.4 6.8 + - - +
284A LEU* 1.3 77.6 - - - +
286A ASN* 1.3 63.1 + - - +
288A VAL* 3.5 6.2 + - - +
289A GLU* 3.0 25.3 + - - +
322A ARG* 2.4 40.7 + - - -
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Residues in contact with ASN 286 (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 ASP* 3.2 31.9 + - - +
285A ASP* 1.3 78.1 - - - +
287A ALA* 1.3 63.8 + - - +
289A GLU* 3.3 4.2 + - - +
290A PHE* 3.0 49.5 + - - -
433A PHE* 4.1 6.7 - - - -
455A ASN* 3.1 35.4 + - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 4.0 23.3 - - + -
282A ALA* 4.8 0.9 - - + -
283A ASP 3.0 17.4 + - - +
284A LEU* 3.6 5.6 - - - +
286A ASN* 1.3 74.2 - - - +
288A VAL* 1.3 65.1 + - - +
290A PHE* 4.4 0.3 - - - +
291A ALA* 3.0 29.1 + - - +
319A PHE* 3.9 6.1 - - + -
433A PHE* 3.7 35.7 - - + -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 2.8 28.6 + - + +
285A ASP* 3.7 6.7 - - - +
287A ALA* 1.3 73.3 - - - +
289A GLU* 1.3 61.0 + - + +
291A ALA* 4.0 0.7 - - - +
292A HIS* 3.0 29.2 + - + +
319A PHE* 3.6 33.4 - - + +
322A ARG* 4.0 44.9 - - + +
323A SER* 4.0 16.3 + - - +
326A ARG* 5.1 7.6 - - + -
406A GLN* 5.6 0.2 + - - -
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Residues in contact with GLU 289 (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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285A ASP 3.0 18.9 + - - +
286A ASN* 3.9 4.5 - - - +
287A ALA 3.3 0.2 - - - -
288A VAL* 1.3 77.8 - - + +
290A PHE* 1.3 61.2 + - + +
292A HIS* 3.3 3.4 + - - +
293A HIS* 2.4 68.1 + - + -
326A ARG* 3.4 33.2 + - - +
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Residues in contact with PHE 290 (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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286A ASN* 3.0 48.3 + - - +
289A GLU* 1.3 76.7 - - + +
291A ALA* 1.3 60.0 + - - +
293A HIS* 4.0 6.9 - + + +
294A GLY* 2.8 27.7 + - - -
433A PHE* 4.0 16.6 - - + -
455A ASN 3.8 8.5 - - - -
456A CYS* 3.7 25.6 - - + -
457A TYR* 3.3 36.7 - - - +
459A VAL* 4.9 5.2 - - + -
601A 3ST 5.2 1.7 - - - +
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Residues in contact with ALA 291 (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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276A CYS* 4.8 10.1 - - - -
278A VAL* 5.8 0.7 - - + -
287A ALA 3.0 20.0 + - - +
288A VAL 4.0 0.7 - - - +
290A PHE* 1.3 73.9 - - - +
292A HIS* 1.3 64.0 + - - +
294A GLY* 3.6 2.0 - - - -
295A VAL* 3.2 23.2 + - - +
306A ALA* 4.2 6.8 - - - +
309A ILE* 3.7 28.8 - - + +
319A PHE* 4.0 15.0 - - + -
406A GLN* 4.0 5.5 + - - +
433A PHE* 4.7 5.3 - - + -
457A TYR* 5.3 0.9 - - - -
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Residues in contact with HIS 292 (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* 3.0 20.6 + - + +
289A GLU* 3.4 4.9 - - - +
291A ALA* 1.3 74.3 - - - +
293A HIS* 1.3 79.6 + + - +
295A VAL 3.1 2.9 + - - -
296A PHE* 2.9 55.1 + + - +
323A SER* 4.6 5.8 + - - +
326A ARG* 3.4 46.4 - - + +
327A ALA* 3.8 11.1 + - - -
330A TYR* 2.5 42.1 + + - -
406A GLN* 4.1 12.7 + - - +
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Residues in contact with HIS 293 (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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289A GLU* 2.4 55.8 + - + +
290A PHE* 4.1 7.4 - + + +
292A HIS* 1.3 86.6 - + - +
294A GLY* 1.3 63.7 + - - +
296A PHE* 4.5 1.3 - - - +
297A TYR* 2.9 41.3 + - + +
326A ARG* 3.4 23.4 + - - -
330A TYR* 4.7 3.8 + - - -
601A 3ST 3.5 17.1 - - - +
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Residues in contact with GLY 294 (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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290A PHE 2.8 20.1 + - - -
291A ALA 3.6 3.4 - - - -
292A HIS 3.1 0.4 - - - -
293A HIS* 1.3 77.1 - - - +
295A VAL* 1.3 56.8 + - - +
297A TYR 4.8 0.2 + - - -
302A CYS* 5.5 0.2 - - - +
305A ALA* 3.4 3.8 - - - +
306A ALA* 3.2 19.2 + - - -
457A TYR* 3.6 16.6 - - - -
601A 3ST 3.2 29.3 + - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA 3.2 9.3 + - - +
292A HIS 3.1 5.5 + - - +
294A GLY* 1.3 75.6 - - - +
296A PHE* 1.3 95.5 + - + +
297A TYR 3.5 0.9 - - - -
300A GLY* 3.3 24.1 - - - -
305A ALA* 4.5 7.5 - - + +
306A ALA 3.6 30.3 - - - +
307A SER* 4.1 9.6 - - - +
403A GLY 4.4 3.6 - - - +
405A VAL 3.6 24.0 - - - +
406A GLN* 3.7 18.8 - - + +
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Residues in contact with PHE 296 (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* 2.9 45.5 + + + +
293A HIS* 4.9 1.1 - - - -
295A VAL* 1.3 97.2 - - + +
297A TYR* 1.3 69.3 + - - +
298A HIS 3.2 0.7 + - - -
299A GLN* 3.1 14.2 + - - -
300A GLY 3.6 3.2 + - - +
327A ALA* 4.3 9.2 - - + -
330A TYR* 3.8 23.5 + + + +
342A GLN* 5.5 1.5 - - - +
384A PRO* 3.7 18.8 - - + -
385A THR 3.7 19.1 - - - -
386A VAL* 4.1 7.6 - - + -
404A PRO* 3.6 40.2 - - + -
405A VAL 4.2 0.7 - - - -
406A GLN* 3.9 20.2 - - + -
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Residues in contact with TYR 297 (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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117A ASN* 3.7 29.1 - - + +
121A ASN* 3.0 36.5 + - - +
122A ASP* 4.5 2.8 + - - -
171A PHE* 4.1 11.2 - + - -
293A HIS* 2.9 30.7 + - + +
295A VAL 3.5 1.6 - - - +
296A PHE* 1.3 75.6 - - - +
298A HIS* 1.3 76.1 + - + +
300A GLY* 3.0 13.5 + - - -
302A CYS* 3.6 15.4 - - - -
601A 3ST 3.4 72.7 - + + +
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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