Contacts of the helix formed by residues 257 - 273 (chain A) in PDB entry 4H1V
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ARG* 3.9 0.2 - - - -
255A LYS 3.2 6.5 + - - -
256A LYS* 1.3 77.1 - - - +
258A VAL* 1.3 59.9 + - - +
259A THR* 3.9 11.0 + - - -
260A ASP* 2.9 45.7 + - - +
261A SER* 3.0 10.0 + - - -
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Residues in contact with VAL 258 (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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47A GLY* 3.4 33.9 - - - +
48A ARG* 5.3 2.2 - - - -
247A ARG* 3.3 26.9 - - - +
257A SER* 1.3 73.6 - - - +
259A THR* 1.3 67.6 + - + +
260A ASP 3.2 0.2 - - - -
261A SER* 3.2 8.8 + - - +
262A ILE* 3.0 44.0 + - + +
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Residues in contact with THR 259 (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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257A SER* 4.2 9.8 + - - +
258A VAL* 1.3 88.1 - - + +
260A ASP* 1.3 67.8 + - - +
262A ILE* 4.0 9.6 - - - +
263A ARG* 3.3 26.2 + - - +
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Residues in contact with ASP 260 (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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256A LYS* 4.1 15.9 - - + +
257A SER* 2.9 28.2 + - - +
259A THR* 1.3 84.0 + - - +
261A SER* 1.3 60.9 + - - +
262A ILE 3.2 0.4 - - - -
263A ARG* 3.0 36.3 + - - +
264A ASP* 3.0 33.2 + - - +
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Residues in contact with SER 261 (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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245A VAL 4.9 2.8 - - - +
246A ASN 6.0 0.4 - - - -
247A ARG* 3.3 41.2 - - - +
256A LYS* 4.0 22.6 - - - +
257A SER 3.0 9.2 + - - -
258A VAL* 3.2 12.6 + - - +
260A ASP* 1.3 75.3 - - - +
262A ILE* 1.3 67.6 + - - +
264A ASP* 3.8 2.9 - - - +
265A GLU* 3.1 22.7 + - - +
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Residues in contact with ILE 262 (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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258A VAL* 3.0 34.5 + - + +
259A THR* 4.0 9.9 - - - +
260A ASP 3.2 0.2 - - - -
261A SER* 1.3 80.0 + - - +
263A ARG* 1.3 61.3 + - + +
265A GLU* 3.3 14.0 + - - +
266A TYR* 3.0 26.2 + - + +
282A THR* 5.8 6.7 - - + -
283A LYS* 3.7 49.8 - - + +
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Residues in contact with ARG 263 (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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259A THR* 3.3 15.8 + - - +
260A ASP* 3.0 43.8 + - - +
262A ILE* 1.3 80.6 - - + +
264A ASP* 1.3 85.6 + - - +
266A TYR* 3.5 11.1 - - + +
267A ALA* 2.7 36.4 + - - +
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Residues in contact with ASP 264 (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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245A VAL* 6.2 0.2 - - - -
256A LYS* 3.4 25.0 + - - +
260A ASP* 3.0 16.1 + - - +
261A SER* 3.8 7.4 - - - +
262A ILE 3.3 0.2 - - - -
263A ARG* 1.3 105.3 + - - +
265A GLU* 1.3 59.6 + - - +
267A ALA* 3.9 5.3 - - - +
268A PHE* 3.0 29.5 + - - +
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Residues in contact with GLU 265 (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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244A VAL* 3.5 5.7 - - - +
245A VAL* 2.9 50.9 + - + +
261A SER 3.1 14.9 + - - +
262A ILE* 3.5 15.5 - - - +
263A ARG 3.3 0.2 - - - -
264A ASP* 1.3 73.7 - - - +
266A TYR* 1.3 59.8 + - - +
268A PHE* 3.2 7.7 + - - +
269A LEU* 2.9 38.9 + - + +
281A GLY* 3.6 4.6 - - - -
282A THR* 3.1 49.0 + - - -
283A LYS* 4.7 4.7 + - - +
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Residues in contact with TYR 266 (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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262A ILE* 3.0 16.3 + - + +
263A ARG* 3.5 13.5 - - + +
265A GLU* 1.3 78.4 - - - +
267A ALA* 1.3 60.8 + - + +
269A LEU* 3.1 11.2 + - + +
270A GLN* 2.9 71.0 + - + +
277A ALA 5.9 3.1 - - - -
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Residues in contact with ALA 267 (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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263A ARG 2.7 22.3 + - - +
264A ASP* 3.9 6.5 - - - +
266A TYR* 1.3 79.1 - - + +
268A PHE* 1.3 62.3 + - - +
270A GLN* 3.4 6.1 + - - +
271A LYS* 3.0 24.6 + - - +
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Residues in contact with PHE 268 (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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217A LEU* 3.4 46.0 - - + -
218A ASP* 3.7 16.4 - - + -
245A VAL* 3.8 19.3 - - + -
264A ASP 3.0 18.4 + - - +
265A GLU* 3.5 6.3 - - - +
267A ALA* 1.3 76.8 - - - +
269A LEU* 1.3 64.5 + - + +
271A LYS* 3.4 4.7 + - + +
272A LYS* 2.9 63.9 + - + +
273A TYR* 4.1 14.1 - + - -
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Residues in contact with LEU 269 (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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217A LEU* 4.0 21.8 - - + -
230A LEU* 5.8 0.9 - - + -
243A GLY 4.6 1.1 - - - +
244A VAL* 5.7 0.2 - - - -
245A VAL* 5.3 1.8 - - + -
265A GLU* 2.9 27.5 + - + +
266A TYR* 3.1 11.9 + - + +
268A PHE* 1.3 80.0 - - + +
270A GLN* 1.3 59.6 + - - +
273A TYR* 2.8 58.5 + - + +
277A ALA* 3.9 17.7 - - + +
280A ASN* 3.7 19.5 - - + +
281A GLY* 3.6 35.9 - - - +
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Residues in contact with GLN 270 (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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266A TYR* 2.9 63.9 + - + +
267A ALA* 3.7 7.2 - - - +
268A PHE 3.4 0.2 - - - -
269A LEU* 1.3 79.4 - - - +
271A LYS* 1.3 61.6 + - - +
274A PRO* 3.6 23.9 + - - +
277A ALA* 3.3 28.1 - - - +
278A ASN* 5.1 1.0 - - - +
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Residues in contact with LYS 271 (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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267A ALA 3.0 18.0 + - - +
268A PHE* 3.8 4.5 - - - +
269A LEU 3.2 0.2 - - - -
270A GLN* 1.3 79.3 - - - +
272A LYS* 1.3 76.9 + - + +
274A PRO* 4.3 6.6 - - - +
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Residues in contact with LYS 272 (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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224A THR 5.9 0.8 + - - -
225A ASP* 5.1 7.8 - - + +
227A MET* 3.6 16.6 - - - +
268A PHE* 2.9 48.2 + - + +
271A LYS* 1.3 93.3 - - + +
273A TYR* 1.3 85.4 + - + +
274A PRO* 3.7 3.5 - - - +
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Residues in contact with TYR 273 (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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217A LEU* 4.0 28.6 + - + +
220A MET* 4.4 5.2 - - - -
224A THR 5.2 0.2 + - - -
225A ASP* 3.9 22.7 - - + +
226A ALA 3.7 34.1 + - - -
227A MET* 4.1 14.6 - - + -
230A LEU* 3.4 31.9 - - + -
268A PHE* 4.1 16.1 - + - -
269A LEU* 2.8 39.9 + - + +
272A LYS* 1.3 96.8 - - + +
274A PRO* 1.3 61.1 - - - +
275A SER* 3.4 2.0 - - - -
276A LEU* 3.9 4.3 - - + -
277A ALA* 2.9 23.6 + - - +
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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