Contacts of the helix formed by residues 264 - 278 (chain F) in PDB entry 4HHM
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 ASP 264 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222F GLN* 4.1 19.7 - - - +
248F GLY* 5.4 0.2 - - - -
249F GLN 3.5 8.1 + - - +
262F ALA 3.4 5.8 + - - +
263F GLY* 1.3 67.6 - - - -
265F LEU* 1.3 64.1 + - - +
266F ARG* 3.6 7.1 + - - +
267F ALA* 3.0 36.3 + - + +
268F ALA* 3.1 19.8 + - - +
250H SER* 6.1 0.5 - - - -
263H GLY 4.6 8.5 - - - +
264H ASP* 5.5 7.3 - - - +
265H LEU 5.8 0.2 + - - -
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Residues in contact with LEU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F GLY* 3.6 25.1 - - - +
263F GLY 3.1 7.7 + - - -
264F ASP* 1.3 70.3 + - - +
266F ARG* 1.3 59.6 + - - +
268F ALA* 2.9 21.1 + - - +
269F PHE* 3.0 11.5 + - - +
313F LEU* 4.6 11.4 - - + +
383F LEU* 4.5 6.1 - - + -
264H ASP* 5.9 0.2 + - - -
265H LEU* 3.6 26.5 - - + +
266H ARG* 3.8 19.4 - - + +
380H MET* 3.7 17.7 - - + -
383H LEU* 3.4 32.8 - - + -
384H LEU* 4.0 22.7 - - + -
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Residues in contact with ARG 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E SER* 5.3 2.6 - - - +
264F ASP* 3.4 6.1 + - - +
265F LEU* 1.3 80.2 - - - +
267F ALA* 1.3 64.0 + - - +
269F PHE* 2.9 20.6 + - - +
270F TRP* 3.0 43.6 + - + +
376F ASP* 2.7 51.2 + - - -
379F ALA* 4.4 1.4 - - - +
380F MET* 3.7 39.1 - - - +
383F LEU* 3.8 17.9 - - + +
262H ALA* 4.3 16.2 - - - +
263H GLY 4.3 11.9 + - - +
265H LEU* 3.9 26.2 - - + +
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Residues in contact with ALA 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 6.1 0.9 - - + -
222F GLN* 4.0 13.0 - - - +
228F PHE* 5.6 1.8 - - + +
229F PRO* 3.5 22.6 - - + +
264F ASP* 3.0 39.7 + - + +
266F ARG* 1.3 76.7 - - - +
268F ALA* 1.3 60.2 + - - +
270F TRP* 4.5 5.2 - - - -
271F LEU* 3.2 23.0 + - - +
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Residues in contact with ALA 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 6.5 0.4 - - - -
260F PHE* 3.9 22.8 - - + -
261F GLY* 4.4 12.1 - - - +
262F ALA 5.6 0.7 - - - +
264F ASP 3.1 10.7 + - - +
265F LEU* 2.9 17.1 + - - +
267F ALA* 1.3 76.0 - - - +
269F PHE* 1.3 63.3 + - - +
271F LEU* 3.2 4.6 + - - +
272F VAL* 3.0 28.4 + - - +
313F LEU* 3.5 18.4 - - + -
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Residues in contact with PHE 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LEU 3.0 9.5 + - - +
266F ARG* 2.9 13.9 + - - +
268F ALA* 1.3 76.1 - - - +
270F TRP* 1.3 100.7 + + - +
271F LEU 3.2 0.3 + - - -
272F VAL* 3.2 2.8 + - - +
273F ASP* 2.9 31.0 + - + +
313F LEU* 3.7 21.2 - - + +
316F ARG* 3.7 12.6 - - + -
317F ALA* 3.4 40.4 - - + -
320F PHE* 4.3 14.8 - + + -
379F ALA* 4.4 16.6 - - + -
383F LEU* 3.6 37.0 - - + -
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Residues in contact with TRP 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLY* 3.4 35.8 - - - +
147E ALA* 3.4 30.3 - - + -
229F PRO* 3.9 22.4 - - + +
266F ARG* 3.0 50.0 + - + +
267F ALA* 4.2 3.1 - - - +
269F PHE* 1.3 95.3 - + - +
271F LEU* 1.3 57.0 + - - +
273F ASP* 3.5 15.7 - - - +
274F LEU* 3.0 27.4 + - - +
320F PHE* 4.2 4.7 - + - -
321F ARG* 4.1 11.7 - - - -
376F ASP* 3.9 9.6 - - - -
379F ALA* 3.6 33.0 - - + -
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Residues in contact with LEU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 3.9 4.0 - - + -
228F PHE* 3.6 35.7 - - + -
229F PRO* 3.9 12.5 - - + +
232F ILE* 4.1 18.2 - - + -
244F ILE* 4.3 2.5 - - + -
246F LEU* 3.7 22.0 - - + -
260F PHE* 3.9 19.3 - - + -
267F ALA 3.2 20.0 + - - +
268F ALA* 3.4 4.7 - - - +
269F PHE 3.1 0.4 - - - -
270F TRP* 1.3 75.4 - - - +
272F VAL* 1.3 60.9 + - + +
274F LEU* 3.4 3.1 + - + +
275F LEU* 3.0 47.1 + - + +
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Residues in contact with VAL 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F PHE* 3.6 26.0 - - + -
268F ALA 3.0 16.6 + - - +
269F PHE 3.8 3.1 - - - +
271F LEU* 1.3 73.7 - - + +
273F ASP* 1.3 68.3 + - - +
275F LEU* 3.2 1.6 + - - +
276F GLU* 2.9 35.1 + - + +
310F TYR* 3.7 35.0 - - + -
313F LEU* 3.9 15.9 - - + +
314F LYS* 3.5 35.0 - - + +
317F ALA* 5.0 0.4 - - + -
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Residues in contact with ASP 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F PHE* 2.9 19.8 + - + +
270F TRP* 3.5 22.5 - - + +
272F VAL* 1.3 77.2 - - - +
274F LEU* 1.3 62.9 + - - +
276F GLU* 4.0 1.8 - - - +
277F SER* 2.9 30.9 + - - -
317F ALA* 3.8 24.2 - - + +
320F PHE* 4.6 1.9 - - - -
321F ARG* 2.6 55.7 + - - +
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Residues in contact with LEU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ASP* 5.8 3.8 - - - +
152E ARG* 4.8 11.0 - - + +
229F PRO* 3.3 31.9 - - + +
232F ILE* 3.5 26.0 - - + -
233F ALA* 3.7 16.6 - - + +
236F LEU* 3.8 16.6 - - + -
270F TRP 3.0 14.8 + - - +
271F LEU* 3.6 5.2 - - + +
272F VAL 3.2 0.2 - - - -
273F ASP* 1.3 84.2 - - - +
275F LEU* 1.3 59.4 + - - +
277F SER* 3.5 6.8 + - - +
278F ALA* 3.0 35.7 + - + +
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Residues in contact with LEU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F ILE* 4.2 13.5 - - + -
236F LEU* 4.6 3.1 - - + -
241F LEU* 3.8 29.4 - - + -
244F ILE* 4.4 11.4 - - + -
246F LEU* 4.7 8.3 - - + -
271F LEU* 3.0 41.2 + - + +
272F VAL 3.2 3.3 + - - +
274F LEU* 1.3 76.9 - - - +
276F GLU* 1.3 60.1 + - - +
278F ALA* 4.0 2.0 - - - -
279F GLY 3.3 1.7 + - - -
280F TRP* 3.1 54.5 + - + +
284F ARG* 3.7 16.2 + - + +
310F TYR* 4.1 17.9 - - + +
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Residues in contact with GLU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F VAL* 2.9 31.9 + - + +
273F ASP* 4.0 2.9 - - - +
275F LEU* 1.3 73.7 - - - +
277F SER* 1.3 58.0 + - - +
278F ALA 3.0 4.9 - - - -
279F GLY* 3.0 18.8 + - - -
284F ARG* 2.8 19.7 + - - +
310F TYR* 2.6 27.4 + - - -
314F LYS* 3.6 38.2 + - + +
317F ALA* 5.9 2.2 - - + -
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Residues in contact with SER 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 4.8 2.3 + - - -
273F ASP* 2.9 24.3 + - - -
274F LEU* 3.5 9.7 + - - +
276F GLU* 1.3 79.0 - - - +
278F ALA* 1.3 60.1 + - - +
279F GLY 3.3 0.4 + - - -
321F ARG* 5.3 13.7 + - - -
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Residues in contact with ALA 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 3.5 35.7 + - - +
236F LEU* 4.3 18.4 - - + -
274F LEU* 3.0 23.4 + - + +
275F LEU* 4.0 4.3 - - - +
276F GLU 3.0 0.4 - - - -
277F SER* 1.3 78.1 - - - +
279F GLY* 1.3 64.0 - - - +
280F TRP 4.5 1.8 - - - +
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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