Contacts of the helix formed by residues 328 - 340 (chain A) in PDB entry 4WMI
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 GLY 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A PHE* 2.9 18.9 + - - +
204A PHE* 4.0 12.8 - - - -
205A PHE* 3.6 27.7 - - - -
326A HIS 3.5 1.2 + - - -
327A LEU* 1.3 73.0 - - - +
329A ASP* 1.3 66.5 + - - -
331A ASP* 3.1 14.4 + - - +
332A PHE 3.2 9.2 + - - -
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Residues in contact with ASP 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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204A PHE* 3.1 22.6 + - - +
205A PHE* 4.0 2.6 - - - -
207A SER* 2.8 31.3 + - - +
208A VAL* 3.8 20.6 - - + -
223A GLN* 4.2 6.8 + - - -
289A SER* 3.6 17.7 + - - -
292A MET* 3.5 16.1 - - - +
327A LEU 3.7 4.9 - - - +
328A GLY* 1.3 70.4 - - - -
330A GLN* 1.3 77.6 + - - +
332A PHE* 3.2 3.0 + - - +
333A PHE* 2.9 31.7 + - + -
3B XYS 5.1 2.4 + - - -
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 5.9 1.1 - - - -
255A GLU* 3.7 3.0 + - - -
260A TYR* 3.1 20.1 + - - +
287A PHE* 3.0 28.7 + - + +
288A ASN* 3.4 3.9 - - - +
289A SER* 3.0 38.4 + - - +
327A LEU* 3.5 22.0 - - + +
328A GLY 3.2 0.4 - - - -
329A ASP* 1.3 83.2 + - - +
331A ASP* 1.3 56.0 + - - +
333A PHE* 4.1 5.0 - - - +
334A THR* 2.9 34.1 + - - -
2B XYS 2.9 24.0 + - - -
3B XYS 3.0 24.4 - - - -
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Residues in contact with ASP 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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191A PHE* 3.5 19.6 - - + +
260A TYR* 2.7 36.7 + - - -
323A PHE* 3.5 17.0 - - + -
325A GLY* 3.1 7.5 - - - -
326A HIS 3.0 13.2 + - - -
327A LEU* 2.8 37.5 + - - +
328A GLY 3.1 10.1 + - - +
330A GLN* 1.3 77.1 - - - +
332A PHE* 1.3 59.5 + - - +
334A THR* 3.5 3.3 + - - -
335A MET* 2.9 30.3 + - - +
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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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187A MET* 4.0 20.6 - - + -
191A PHE* 3.9 36.4 - + + -
205A PHE* 5.0 0.2 - - + -
208A VAL* 3.7 26.7 - - + -
305A TYR* 4.1 5.8 - - - -
308A LEU* 3.8 25.6 - - + -
309A LEU* 3.8 26.0 - - + -
314A VAL* 4.2 7.4 - - + -
328A GLY 3.2 7.2 + - - +
329A ASP* 3.8 5.2 - - - +
331A ASP* 1.3 74.2 - - - +
333A PHE* 1.3 66.6 + + - +
335A MET* 3.2 6.1 + - + +
336A ILE* 2.9 68.6 + - + +
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Residues in contact with PHE 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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207A SER* 3.2 31.2 - - - -
208A VAL* 3.7 22.4 - - + -
250A ILE* 3.5 33.9 - - + -
252A ILE* 4.2 11.0 - - + -
287A PHE* 3.4 17.9 - - + -
292A MET* 3.7 24.9 - - - -
294A LEU* 4.8 2.5 - - + -
305A TYR* 3.5 15.7 - + - -
329A ASP* 2.9 21.6 + - + +
330A GLN* 4.1 2.7 - - - +
332A PHE* 1.3 86.5 - + - +
334A THR* 1.3 64.4 + - - +
336A ILE* 4.0 1.8 - - + -
337A GLY* 2.9 19.1 + - - -
344A PHE* 3.6 24.4 - + + -
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Residues in contact with THR 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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260A TYR* 3.3 34.7 - - + -
264A PHE* 3.9 6.3 - - + -
286A GLY* 3.7 21.3 - - - -
287A PHE* 3.0 30.8 + - - +
323A PHE* 4.8 0.2 - - + -
330A GLN 2.9 23.0 + - - -
331A ASP 3.6 4.7 - - - +
333A PHE* 1.3 79.0 - - - +
335A MET* 1.3 62.3 + - - +
337A GLY* 3.6 1.6 - - - -
338A MET* 3.2 33.2 + - + +
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Residues in contact with MET 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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191A PHE* 3.7 28.5 - - + -
264A PHE* 4.5 3.4 - - + -
314A VAL* 4.1 13.2 - - - +
317A LEU* 3.7 21.3 - - + +
318A ALA* 3.6 29.4 - - - -
321A TYR* 4.0 19.8 - - + -
323A PHE* 4.2 20.2 - - + -
331A ASP 2.9 18.0 + - - +
332A PHE* 3.2 8.3 + - + +
334A THR* 1.3 73.9 - - - +
336A ILE* 1.3 83.1 + - + +
338A MET* 3.0 24.2 + - - +
339A GLU* 3.5 6.6 + - - +
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Residues in contact with ILE 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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305A TYR* 4.0 17.7 - - + -
308A LEU* 4.2 19.7 - - + +
317A LEU* 4.2 23.8 - - + -
332A PHE* 2.9 66.6 + - + +
333A PHE* 3.7 7.6 - - + +
335A MET* 1.3 77.9 - - + +
337A GLY* 1.3 53.6 + - - +
339A GLU* 3.3 2.2 + - - +
340A HIS* 2.7 38.3 + - - +
343A LEU* 4.2 11.9 - - + -
344A PHE* 3.8 21.5 - - + -
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Residues in contact with GLY 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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284A LEU* 5.0 5.5 - - - +
287A PHE* 4.1 9.9 - - - -
333A PHE 2.9 17.9 + - - -
334A THR 3.6 2.7 - - - -
335A MET 3.1 0.2 - - - -
336A ILE* 1.3 76.9 - - - +
338A MET* 1.3 64.0 + - - +
340A HIS 4.0 2.5 - - - -
341A PRO* 3.4 24.8 - - - +
344A PHE* 3.6 21.1 - - - -
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Residues in contact with MET 338 (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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260A TYR* 4.9 0.4 - - + -
264A PHE* 3.8 36.6 - - + -
276A VAL* 3.9 22.1 - - + +
277A GLY* 4.0 1.8 - - - +
284A LEU* 3.4 57.4 - - - +
285A PRO 4.6 0.7 - - - -
286A GLY* 4.0 9.2 - - - +
321A TYR* 3.7 23.3 + - + +
334A THR* 3.2 25.0 + - + +
335A MET 3.0 10.3 + - - +
337A GLY* 1.3 79.4 - - - +
339A GLU* 1.3 62.9 + - - +
341A PRO* 3.9 5.7 - - - +
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Residues in contact with GLU 339 (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 TRP* 6.2 0.2 - - - -
317A LEU* 3.6 34.0 - - + +
320A LYS* 2.8 24.8 + - - +
321A TYR* 2.8 30.3 + - + +
335A MET 3.5 4.6 + - - +
336A ILE 3.3 5.5 + - - +
338A MET* 1.3 80.0 - - - +
340A HIS* 1.3 92.5 + - + +
341A PRO* 3.5 6.4 - - - +
342A GLU* 4.2 1.4 - - - +
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Residues in contact with HIS 340 (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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304A LEU* 3.8 28.4 - - + +
308A LEU* 3.8 24.0 - - + +
313A TRP* 6.4 2.0 - + - -
317A LEU* 5.2 0.2 - - + -
336A ILE 2.7 20.4 + - - +
337A GLY 3.9 0.4 - - - -
339A GLU* 1.3 107.4 + - + +
341A PRO* 1.3 66.6 - - - +
342A GLU* 3.1 28.1 + - - +
343A LEU* 3.2 31.3 + - + +
344A PHE* 3.9 3.8 - - - -
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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