Contacts of the helix formed by residues 289 - 303 (chain A) in PDB entry 2W7P
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 SER 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.3 0.9 - - - -
287A GLY 3.7 0.4 - - - -
288A THR* 1.3 83.8 + - - +
290A ALA* 1.3 65.3 + - - +
291A GLN* 3.0 25.6 + - - +
292A GLU* 3.0 15.1 + - - +
293A VAL* 3.0 19.6 + - - +
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Residues in contact with ALA 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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102A THR* 4.0 12.6 - - + -
204A ILE* 4.0 4.0 - - + +
208A LEU* 3.8 32.1 - - + +
288A THR 3.8 0.4 + - - -
289A SER* 1.3 74.3 - - - +
291A GLN* 1.3 63.4 + - - +
293A VAL* 3.9 4.8 - - - +
294A VAL* 3.1 27.7 + - - +
313A ILE* 4.0 4.8 - - + +
334A GLN* 3.7 21.5 - - - +
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Residues in contact with GLN 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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289A SER* 2.9 15.0 + - - +
290A ALA* 1.3 81.0 - - - +
292A GLU* 1.3 56.2 + - + +
294A VAL* 3.6 0.5 + - - +
295A LYS* 3.1 32.8 + - + +
313A ILE* 3.7 5.2 - - - +
332A GLN* 3.2 38.4 + - - +
333A TYR* 5.2 1.2 - - - -
334A GLN* 3.4 45.0 + - - +
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Residues in contact with GLU 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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285A VAL 4.3 2.9 - - - +
286A PHE* 3.3 16.7 - - + +
287A GLY* 2.5 49.6 + - - +
288A THR 4.4 0.4 - - - +
289A SER* 3.0 20.6 + - - +
291A GLN* 1.3 75.2 - - + +
293A VAL* 1.3 68.3 + - - +
294A VAL 3.1 1.6 - - - -
295A LYS* 2.8 29.8 + - - +
296A GLU* 2.8 24.9 + - - +
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Residues in contact with VAL 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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188A TYR* 4.1 16.2 - - + -
204A ILE* 4.2 18.4 - - + -
207A HIS* 3.8 26.0 - - + +
208A LEU* 4.3 12.3 - - + -
211A ARG* 3.5 37.7 - - - +
288A THR 4.3 1.1 - - - +
289A SER 3.0 18.4 + - - +
290A ALA* 3.9 7.2 - - - +
291A GLN 3.5 0.2 - - - -
292A GLU* 1.3 77.1 - - - +
294A VAL* 1.3 64.0 + - - +
296A GLU* 3.2 5.4 + - - +
297A ILE* 3.2 25.0 + - + +
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Residues in contact with VAL 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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104A VAL* 3.5 39.5 - - + -
106A ILE* 6.5 0.2 - - + -
204A ILE* 4.6 3.6 - - + -
290A ALA 3.1 17.4 + - - +
291A GLN 3.9 2.9 - - - +
293A VAL* 1.3 79.9 - - - +
295A LYS* 1.3 57.0 + - - +
297A ILE* 3.0 15.2 + - + +
298A ARG* 2.8 29.3 + - + +
311A ALA* 3.9 22.0 - - + -
313A ILE* 4.0 13.9 - - + -
332A GLN* 2.9 24.9 - - - +
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Residues in contact with LYS 295 (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 PHE* 3.5 13.3 - - + -
291A GLN* 3.1 26.4 + - + +
292A GLU* 2.8 31.2 + - - +
294A VAL* 1.3 76.1 - - - +
296A GLU* 1.3 56.2 + - - +
298A ARG* 3.5 17.3 + - - +
299A PHE* 3.1 27.0 + - - +
332A GLN* 3.6 21.5 - - - +
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Residues in contact with GLU 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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188A TYR* 2.7 28.3 + - - +
207A HIS* 5.4 0.7 - - - -
211A ARG* 3.2 34.1 + - - -
214A TRP* 6.2 0.2 - - - -
218A LYS 4.7 4.0 - - - +
219A ARG* 4.5 6.4 - - - -
221A TYR* 3.2 36.5 + - + -
286A PHE* 3.1 32.4 - - + +
292A GLU 2.8 11.1 + - - +
293A VAL* 3.4 9.9 - - - +
295A LYS* 1.3 72.9 - - - +
297A ILE* 1.3 54.3 + - - +
299A PHE* 3.2 1.6 + - - +
300A ARG* 2.7 33.7 + - - +
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Residues in contact with ILE 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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104A VAL* 5.7 2.0 - - + -
106A ILE* 3.9 14.4 - - + -
184A ILE* 5.1 4.3 - - + -
185A LEU* 3.9 22.7 - - + -
188A TYR* 3.7 42.8 - - + -
202A LEU* 4.6 13.7 - - + -
204A ILE* 4.9 4.3 - - + -
293A VAL* 3.2 20.9 - - + +
294A VAL* 3.0 19.9 + - + +
296A GLU* 1.3 73.8 - - - +
298A ARG* 1.3 61.9 + - + +
299A PHE 2.9 6.1 + - - -
300A ARG* 4.2 4.9 - - - +
301A ILE* 3.2 31.0 + - + +
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Residues in contact with ARG 298 (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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106A ILE* 5.9 4.0 - - + -
294A VAL* 2.8 19.5 + - + +
295A LYS* 3.9 21.2 - - - +
297A ILE* 1.3 78.0 - - + +
299A PHE* 1.3 58.4 + - - +
301A ILE* 4.3 6.4 - - - +
302A GLU* 3.5 19.6 + - - +
307A LEU 5.4 0.7 - - - +
308A THR* 5.8 3.5 - - - +
309A ALA* 3.4 30.1 + - + +
310A SER 5.2 0.2 - - - -
311A ALA* 4.4 8.3 - - + -
330A ASN* 2.9 40.6 + - - +
331A GLY* 3.5 20.2 + - - +
332A GLN* 2.9 38.8 + - - +
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Residues in contact with PHE 299 (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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221A TYR* 3.8 28.5 - + + -
222A PHE 4.1 9.2 - - - -
223A ILE* 4.8 6.1 - - + -
284A VAL* 4.2 18.4 - - + -
286A PHE* 3.7 22.7 - + + -
295A LYS 3.1 17.0 + - - +
296A GLU 3.3 4.9 - - - +
297A ILE 2.9 0.2 - - - -
298A ARG* 1.3 78.3 - - - +
300A ARG* 1.3 73.0 + - - +
301A ILE 3.0 1.3 - - - -
302A GLU* 3.0 19.5 + - + +
303A GLN* 3.1 52.2 + - + +
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Residues in contact with ARG 300 (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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183A GLU 5.5 0.2 + - - -
184A ILE* 3.7 33.5 - - + +
187A ASP* 3.3 30.5 + - - +
188A TYR* 3.2 38.5 + - - -
221A TYR* 3.5 45.6 + - + -
296A GLU 2.7 21.3 + - - +
297A ILE* 3.5 2.7 + - - +
299A PHE* 1.3 78.3 - - + +
301A ILE* 1.3 63.0 + - - +
303A GLN* 3.7 6.9 - - - +
304A LYS* 3.4 18.9 - - - +
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Residues in contact with ILE 301 (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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106A ILE* 4.6 22.0 - - + -
108A MET* 4.1 15.7 - - + -
181A VAL* 3.1 39.9 - - + +
184A ILE* 3.7 17.7 - - + +
185A LEU* 5.2 0.2 - - + -
297A ILE* 3.2 32.3 + - + +
298A ARG* 4.3 5.8 - - - +
299A PHE 3.0 0.4 - - - -
300A ARG* 1.3 74.4 - - - +
302A GLU* 1.3 69.1 + - - +
304A LYS* 3.0 10.4 + - - +
305A THR* 2.7 31.3 + - + +
307A LEU 4.1 8.5 - - - +
308A THR* 5.7 0.9 - - - -
309A ALA* 5.5 3.8 - - + +
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Residues in contact with GLU 302 (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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298A ARG 3.5 15.0 + - - +
299A PHE* 3.0 15.0 + - + +
301A ILE* 1.3 78.0 - - - +
303A GLN* 1.3 67.1 + - + +
304A LYS 2.8 7.6 + - - -
306A THR* 2.7 57.2 + - - +
307A LEU 3.5 12.1 + - - +
308A THR* 3.1 26.6 - - + +
330A ASN* 4.0 5.7 + - - -
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Residues in contact with GLN 303 (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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222A PHE 3.1 13.9 - - - +
223A ILE* 2.6 45.1 + - - +
224A LYS* 4.7 5.9 - - - +
299A PHE* 3.1 41.4 + - + +
300A ARG* 3.7 4.6 - - - +
302A GLU* 1.3 80.0 - - + +
304A LYS* 1.3 62.6 + - - +
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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