Contacts of the helix formed by residues 260 - 269 (chain G) in PDB entry 2W3S
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 HIS 260 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241G TYR* 5.2 3.6 - + - -
255G PHE* 6.3 0.9 - + - -
256G ALA* 2.8 28.5 + - + +
258G GLY 3.1 1.4 + - - -
259G PRO* 1.3 96.8 + - + +
261G PRO* 1.3 60.7 - - - +
262G ALA* 3.1 3.3 - - + +
263G LEU* 2.9 24.4 + - + +
264G ALA 3.0 7.3 + - - -
301G MET* 3.4 36.0 - - + +
341G LEU* 4.6 12.1 - - + +
342G PRO* 2.9 25.6 + - + -
343G LYS 4.0 4.2 + - - -
344G SER 3.6 1.8 - - - -
345G ALA* 3.4 42.0 + - + +
348G LEU* 5.0 2.6 - - - +
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Residues in contact with PRO 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G ALA 3.4 3.5 - - - +
257G GLU* 4.3 9.9 - - - +
258G GLY 3.5 13.7 - - - +
259G PRO 3.8 3.6 - - - +
260G HIS* 1.3 87.2 - - - +
262G ALA* 1.3 56.7 + - - +
263G LEU 3.3 0.2 - - - -
264G ALA* 3.8 6.3 - - + -
265G GLY* 2.9 27.2 + - - -
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Residues in contact with ALA 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G HIS* 3.0 2.3 + - - +
261G PRO* 1.3 80.8 - - - +
263G LEU* 1.3 61.0 + - - +
265G GLY* 4.5 0.6 - - - -
266G LEU 3.6 11.4 + - - -
348G LEU* 3.1 50.3 - - + +
349G ARG* 4.3 8.7 - - - -
350G CYS* 3.3 20.4 - - - +
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Residues in contact with LEU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252G LEU* 4.1 22.0 - - + -
256G ALA* 3.9 18.8 - - + -
260G HIS* 2.9 12.0 + - + +
262G ALA* 1.3 76.8 - - - +
264G ALA* 1.3 61.2 + - - +
266G LEU* 3.3 7.0 + - + +
267G LEU* 3.0 43.8 + - + +
294G GLY* 5.3 2.5 - - - +
297G ALA* 3.8 27.1 - - + -
298G LEU* 3.9 27.6 - - + -
301G MET* 4.0 17.0 - - + -
341G LEU* 4.3 13.0 - - + -
348G LEU* 4.5 1.7 - - + +
350G CYS* 4.5 4.3 - - - -
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Residues in contact with ALA 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ARG* 3.2 46.8 + - + +
256G ALA* 3.7 8.5 - - - +
257G GLU* 3.7 27.6 - - + +
260G HIS 3.0 6.9 + - - +
261G PRO* 4.1 4.9 - - + +
263G LEU* 1.3 76.1 - - - +
265G GLY* 1.3 59.0 + - - +
267G LEU 3.2 0.3 + - - -
268G ARG 3.0 23.6 + - - -
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Residues in contact with GLY 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G PRO 2.9 17.8 + - - -
262G ALA 4.5 0.7 - - - -
264G ALA* 1.3 77.1 - - - +
266G LEU* 1.3 59.1 + - - +
268G ARG* 3.1 26.6 + - - +
269G ARG* 4.0 6.6 + - - +
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Residues in contact with LEU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G ALA 3.6 13.6 + - - +
263G LEU* 3.3 13.8 + - + +
264G ALA 3.2 0.2 - - - -
265G GLY* 1.3 73.2 - - - +
267G LEU* 1.3 69.6 + - + +
268G ARG 3.1 1.8 - - - -
269G ARG* 3.2 23.3 + - - +
270G PHE* 3.7 2.0 + - + +
293G ASP* 3.5 33.2 - - + +
297G ALA* 3.7 22.0 - - + -
350G CYS* 3.6 28.9 - - + +
352G LYS* 4.2 29.7 - - + +
365G CYS* 4.3 14.1 - - - -
367G CYS* 5.0 1.1 - - - -
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Residues in contact with LEU 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G ILE* 3.4 43.1 - - + +
252G LEU* 3.8 24.0 - - + -
253G ARG* 3.4 34.1 - - + +
263G LEU* 3.0 33.0 + - + +
264G ALA 3.2 0.2 + - - -
266G LEU* 1.3 81.7 - - + +
268G ARG* 1.3 68.6 + - - +
270G PHE* 2.9 29.5 + - + +
276G ARG* 3.1 17.0 - - - -
294G GLY* 5.4 8.3 - - - -
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Residues in contact with ARG 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ASP* 3.5 32.6 + - + +
253G ARG* 3.0 41.0 - - - +
264G ALA 3.0 7.8 + - - +
265G GLY* 3.1 19.0 + - - +
267G LEU* 1.3 78.7 - - - +
269G ARG* 1.3 88.1 - - - +
276G ARG* 2.9 30.5 + - - +
358G ASP* 3.9 12.3 + - - -
458G LEU* 3.9 20.4 + - - +
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Residues in contact with ARG 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G GLY 4.6 5.6 - - - +
266G LEU* 3.2 13.2 + - - +
267G LEU 3.1 0.6 - - - -
268G ARG* 1.3 106.9 - - - +
270G PHE* 1.3 56.8 + - - +
271G ALA 4.0 5.1 + - - +
352G LYS* 3.0 70.9 + - + +
354G SER* 3.2 20.6 + - - +
357G PHE* 2.8 53.2 + - - +
358G ASP* 4.2 13.2 - - - +
359G GLN 5.0 4.8 + - - +
360G ASP 4.8 0.7 + - - +
458G LEU* 4.3 9.5 - - - +
639H GLU* 4.1 4.2 + - - -
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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