Contacts of the helix formed by residues 350 - 361 (chain B) in PDB entry 4A8W
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 ALA 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B GLY 3.7 3.1 + - - -
349B TYR* 1.4 72.4 - - - +
351B PRO* 1.4 71.7 - - - +
352B TRP* 3.2 40.6 - - + +
353B TRP* 3.1 17.2 + - + +
354B VAL* 3.1 12.3 + - - +
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Residues in contact with PRO 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LEU* 3.9 21.4 - - + +
345B LEU* 3.7 24.9 - - + +
349B TYR 3.2 6.5 - - - +
350B ALA* 1.4 81.8 - - + +
352B TRP* 1.3 60.8 + - + +
354B VAL* 3.4 2.4 + - - +
355B LYS* 3.0 29.5 + - - +
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Residues in contact with TRP 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU 5.9 1.6 - - - -
174B ALA* 3.7 19.5 - - + -
175B GLU* 3.4 74.7 + - + +
178B GLY* 3.5 7.5 - - - -
179B ASN* 3.4 27.6 - - - +
182B LEU* 3.8 10.1 - - - +
282B PRO* 5.7 0.2 - - + -
350B ALA* 3.4 24.6 - - + +
351B PRO* 1.3 80.8 - - + +
353B TRP* 1.4 100.3 + + + +
355B LYS* 3.5 1.6 + - - +
356B LEU* 3.2 26.7 + - + +
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Residues in contact with TRP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 4.7 6.3 - + - -
282B PRO* 2.9 34.3 + - + +
283B ILE* 4.1 15.1 - - + +
286B VAL* 3.5 41.4 - - + +
344B LEU* 3.9 21.8 - - + -
349B TYR* 4.0 22.4 - + + -
350B ALA* 3.1 17.2 + - + +
352B TRP* 1.4 104.0 - + + +
354B VAL* 1.4 71.9 + - + +
356B LEU* 3.1 9.7 + - + +
357B PHE* 3.0 56.4 + + + -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B CYS* 3.5 42.8 - - + +
344B LEU* 3.9 13.9 - - + -
345B LEU* 3.9 22.7 - - + -
349B TYR* 3.8 23.6 - - + -
350B ALA 3.1 13.5 + - - +
351B PRO 3.4 6.7 + - - +
353B TRP* 1.4 86.0 - - + +
355B LYS* 1.4 50.1 - - - +
357B PHE* 3.2 4.7 + - - +
358B GLU* 2.8 33.6 + - + +
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B GLY 4.2 2.2 - - - +
181B MET* 3.7 39.0 + - + -
182B LEU* 3.8 30.7 + - + +
186B PHE* 3.8 21.8 - - - -
351B PRO 3.0 17.2 + - - +
352B TRP 3.8 5.2 - - - +
353B TRP 3.3 0.2 - - - -
354B VAL* 1.4 72.6 - - - +
356B LEU* 1.4 57.0 + - - +
358B GLU* 3.2 34.5 + - - +
359B THR* 2.6 38.9 + - - -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ALA* 3.5 37.2 - - + +
178B GLY* 3.8 17.9 - - - +
181B MET* 3.7 28.3 - - + -
195B MET* 4.0 15.3 - - - -
279B LEU* 3.7 16.3 - - + +
282B PRO* 4.3 15.0 - - + -
283B ILE* 4.5 7.9 - - + -
352B TRP* 3.2 22.5 + - + +
353B TRP* 3.1 11.9 + - + +
355B LYS* 1.4 74.1 - - - +
357B PHE* 1.3 58.5 + - - +
359B THR* 3.3 3.3 + - - -
360B SER* 3.0 28.4 + - - -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 5.0 7.0 - + - -
283B ILE* 3.9 21.3 - - + +
337B ARG 5.4 0.9 - - - -
340B ILE* 4.2 17.3 - - + -
341B CYS* 4.0 15.5 - - - -
344B LEU* 4.8 7.0 - - + -
353B TRP* 3.0 43.8 + + + +
354B VAL* 3.4 8.1 - - - +
356B LEU* 1.3 73.7 - - - +
358B GLU* 1.4 64.6 + - - +
360B SER* 2.6 23.5 + - - -
361B LEU* 3.6 20.9 + - + +
395B GLN* 3.6 22.7 - - - -
397B ALA* 4.6 8.1 - - + -
401B MET* 3.6 35.9 - - + -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B PHE* 5.7 0.2 - - - -
337B ARG* 3.6 13.1 - - - -
338B ASP* 4.4 8.4 - - - +
341B CYS* 3.6 26.1 - - - +
354B VAL* 2.8 19.4 + - - +
355B LYS* 3.2 41.7 + - - +
357B PHE* 1.4 71.9 - - - +
359B THR* 1.4 59.5 + - - +
361B LEU* 3.0 19.1 + - - -
362B LYS* 3.0 41.0 - - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B MET* 3.6 24.9 - - + -
186B PHE* 3.7 19.5 - - + -
196B GLY* 5.5 1.8 - - - -
279B LEU* 4.8 3.6 - - + -
355B LYS* 2.6 29.4 + - - +
356B LEU 3.3 4.5 + - - -
358B GLU* 1.4 76.0 + - - +
360B SER* 1.4 61.5 + - - +
362B LYS* 3.1 18.1 + - - -
363B LEU* 3.2 23.1 + - + +
385B PRO* 3.8 27.6 - - + -
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TYR* 2.6 36.8 + - - -
279B LEU* 3.9 19.0 - - - +
280B ASN* 5.3 1.1 - - - -
283B ILE* 3.5 25.7 - - - +
356B LEU 3.0 7.8 + - - -
357B PHE 2.6 19.0 + - - -
359B THR* 1.4 73.9 - - - +
361B LEU* 1.3 57.5 + - - +
362B LYS 3.5 0.2 - - - -
363B LEU* 4.8 1.6 - - - -
392B SER* 4.4 1.2 + - - -
395B GLN* 2.7 32.6 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TYR* 6.1 0.2 - - - -
332B TRP* 4.3 15.4 - - + -
337B ARG* 3.1 51.3 + - + -
357B PHE* 3.8 34.3 - - + +
358B GLU 3.0 3.7 + - - +
360B SER* 1.3 78.6 + - - +
362B LYS* 1.4 58.3 + - - +
363B LEU 3.8 0.2 - - - -
387B LEU 3.7 4.0 - - - +
388B GLU* 5.4 0.5 - - - -
389B VAL* 5.6 4.2 + - - +
390B GLY 4.7 12.9 - - - +
391B LEU* 3.8 28.9 - - + -
392B SER* 4.8 8.3 - - - +
395B GLN* 3.8 29.4 - - + +
401B MET* 4.4 4.5 - - + -
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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