Contacts of the helix formed by residues 264 - 275 (chain A) in PDB entry 2IVF
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.1 0.7 - - - -
125A LEU* 4.1 4.0 - - - +
241A ALA* 3.8 11.9 - - - -
257A TRP* 4.2 8.0 - - - -
261A TYR* 3.1 30.1 + - - -
263A SER* 1.3 81.0 + - - +
265A TYR* 1.3 67.4 + - - +
266A HIS* 3.0 10.4 + - - -
267A PHE* 3.0 30.7 + - - +
668A ASN* 2.8 24.2 + - - -
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TRP* 3.8 17.9 - - + -
258A SER* 3.6 40.8 - - - -
261A TYR 2.8 15.7 + - - +
262A PRO 4.1 3.6 - - - +
263A SER 3.8 1.0 - - - -
264A SER* 1.3 76.2 - - - +
266A HIS* 1.3 56.7 + - - +
268A LEU* 2.8 37.2 + - + +
269A SER* 3.4 7.9 + - - -
287A PRO 4.8 0.5 + - - -
288A THR* 3.8 16.6 + - + -
290A PRO* 4.1 10.4 - - - +
291A ALA* 3.3 39.0 + - + +
26B ASN 5.1 0.7 + - - -
27B LYS* 3.8 15.0 - - - -
28B CYS 4.3 2.4 + - - -
29B LEU* 3.6 43.6 - - + +
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Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP 3.2 26.9 + - - -
122A TYR* 4.0 10.0 + - - -
263A SER 3.6 23.3 + - - -
264A SER* 3.0 5.1 + - - -
265A TYR* 1.3 82.5 - - - +
267A PHE* 1.3 79.7 + + - +
269A SER* 3.1 10.2 + - - -
270A GLU* 2.6 72.5 + - - +
231B PRO 3.8 11.3 + - - +
232B GLY* 3.6 19.7 - - - +
233B ARG* 3.1 22.5 - - - -
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Residues in contact with PHE 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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120A VAL* 3.5 27.8 - - + -
121A ASP 3.4 16.6 - - - -
122A TYR* 3.7 35.0 - + - -
241A ALA* 3.3 35.9 - - + +
242A ASP* 3.5 27.6 - - + -
244A LEU* 4.1 6.9 - - + +
245A LEU* 3.9 15.6 - - + +
264A SER* 3.0 21.1 + - - +
266A HIS* 1.3 101.5 - + - +
268A LEU* 1.3 56.6 + - - +
270A GLU* 4.0 4.0 - - - -
271A ALA* 2.8 31.0 + - - +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.7 13.9 - - + +
250A ILE* 3.7 27.1 - - + -
252A MET* 3.9 19.5 - - + -
257A TRP* 4.1 11.7 - - + -
264A SER 4.3 0.4 + - - -
265A TYR* 2.8 21.8 + - + +
267A PHE* 1.3 72.7 - - - +
269A SER* 1.3 63.5 + - - +
271A ALA* 3.4 4.4 + - - +
272A ARG* 3.1 21.7 + - - +
278A VAL* 3.7 34.0 - - + +
288A THR* 3.9 24.2 - - + -
291A ALA* 3.9 20.9 - - + -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.4 13.2 + - - -
266A HIS* 3.1 17.7 + - - -
268A LEU* 1.3 78.5 - - - +
270A GLU* 1.3 59.5 + - - +
272A ARG* 3.3 10.6 - - - +
273A TYR* 3.2 28.1 + - - -
291A ALA* 4.6 9.3 - - - +
26B ASN* 4.2 8.1 - - - -
27B LYS* 3.6 43.7 + - - +
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Residues in contact with GLU 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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120A VAL* 3.3 15.0 - - + +
245A LEU* 4.2 9.0 - - + -
266A HIS* 2.6 47.9 + - - +
267A PHE* 3.9 4.8 + - - +
269A SER* 1.3 69.8 - - - +
271A ALA* 1.3 65.6 + - - +
272A ARG 3.1 0.2 - - - -
273A TYR* 3.2 5.1 + - + +
274A LYS* 3.0 21.8 + - - +
27B LYS* 2.7 38.0 + - - +
233B ARG* 2.8 27.1 + - - -
333B ILE* 3.7 31.6 - - + +
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Residues in contact with ALA 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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244A LEU* 3.6 20.2 - - + +
245A LEU* 3.8 10.4 - - + +
250A ILE* 3.5 29.4 - - + -
267A PHE 2.8 20.7 + - - +
268A LEU 3.4 2.7 + - - +
270A GLU* 1.3 74.6 - - - +
272A ARG* 1.3 61.5 + - - +
274A LYS* 3.3 5.9 + - - +
275A GLY 3.1 6.1 + - - -
276A ALA* 2.8 27.5 + - + +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU 3.1 13.4 + - - +
269A SER* 3.3 13.5 - - - +
271A ALA* 1.3 77.7 - - - +
273A TYR* 1.3 58.0 + - - +
275A GLY* 3.0 12.6 + - - -
276A ALA* 3.5 10.0 - - - +
278A VAL* 3.9 8.0 - - + +
290A PRO 3.4 24.2 + - - -
291A ALA* 3.4 19.4 + - - +
292A ALA 3.3 14.4 + - - -
293A ASP* 3.0 30.1 + - - +
26B ASN* 4.3 9.2 + - - +
276B MET* 3.7 36.4 - - + +
277B GLY 3.2 27.1 + - - +
314B HIS* 5.5 1.6 - - - -
317B ARG* 2.7 42.5 + - - +
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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
----------------------------------------------------------
269A SER 3.2 13.6 + - - -
270A GLU* 3.2 8.8 + - - +
272A ARG* 1.3 78.4 - - + +
274A LYS* 1.3 59.9 + - - +
275A GLY* 3.1 1.3 + - - -
24B ASP* 2.6 40.4 + - - -
26B ASN* 3.1 17.4 + - + +
27B LYS* 3.9 17.9 - - + -
273B VAL* 4.3 0.7 - - - +
276B MET* 3.8 25.1 - - + -
313B LEU* 4.5 3.8 - - + -
317B ARG* 4.0 8.2 - - - +
320B MET* 3.7 6.1 - - - +
329B MET* 3.3 46.6 - - + +
332B LEU* 3.7 41.4 - - + +
333B ILE* 3.7 14.8 - - + -
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Residues in contact with LYS 274 (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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118A ASP 5.1 8.6 + - - -
119A TYR* 5.3 2.6 - - - -
245A LEU* 2.5 54.2 + - + +
246A ASP* 4.5 6.1 + - - -
270A GLU 3.0 12.9 + - - +
271A ALA* 3.5 10.3 - - - +
272A ARG 3.2 0.2 - - - -
273A TYR* 1.3 75.3 - - - +
275A GLY* 1.3 55.8 + - - +
276A ALA 3.7 0.9 - - - +
320B MET* 3.6 38.7 - - + +
321B ARG* 3.7 7.6 + - - -
333B ILE* 3.8 6.5 - - + +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLU* 4.3 3.8 - - - +
272A ARG 3.0 9.7 + - - -
273A TYR 3.1 1.7 - - - -
274A LYS* 1.3 81.3 - - - +
276A ALA* 1.3 67.3 + - - +
277A GLU* 3.5 1.2 + - - +
317B ARG* 4.4 4.7 - - - -
321B ARG* 2.9 50.7 + - - +
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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