Contacts of the helix formed by residues 247 - 267 (chain A) in PDB entry 4P9U
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A VAL* 4.8 6.3 - - + -
244A GLU* 3.4 44.4 + - + +
245A ARG 3.2 0.4 - - - -
246A GLU* 1.3 92.5 - - + +
248A LEU* 1.3 62.2 + - - +
249A PRO* 3.5 2.2 - - - -
250A GLN* 3.3 16.7 - - + +
251A VAL* 3.2 30.2 + - + +
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Residues in contact with LEU 248 (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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110A PRO* 3.6 24.9 - - + +
113A MET* 4.5 8.3 - - + -
114A ARG* 4.7 8.3 - - + +
117A PHE* 3.8 23.8 - - + -
236A LEU* 3.6 30.1 - - + -
239A VAL* 4.0 23.6 - - + +
245A ARG* 3.5 15.1 - - + +
247A HIS* 1.3 74.6 - - - +
249A PRO* 1.4 72.4 - - + +
250A GLN 3.2 0.2 + - - -
251A VAL* 3.2 4.3 + - + +
252A ILE* 3.0 49.0 + - + +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.6 15.5 - - + -
245A ARG 3.6 7.0 - - - +
246A GLU 3.6 16.6 - - - +
248A LEU* 1.4 99.7 - - + +
250A GLN* 1.3 62.9 + - + +
252A ILE* 3.3 5.4 + - + +
253A ARG* 2.9 43.8 + - + +
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU 5.7 1.0 + - - -
247A HIS* 3.3 25.1 - - + +
248A LEU 3.1 0.4 - - - -
249A PRO* 1.3 85.1 - - + +
251A VAL* 1.3 64.0 + - + +
253A ARG* 3.3 5.1 + - - +
254A GLN* 3.0 55.2 + - - +
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Residues in contact with VAL 251 (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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232A PHE* 3.5 24.0 - - + -
235A GLN* 3.6 38.1 - - + +
236A LEU* 4.1 11.7 - - + +
239A VAL* 4.2 17.5 - - + -
247A HIS* 3.2 16.3 + - + +
248A LEU* 3.2 8.0 + - - +
250A GLN* 1.3 81.9 - - + +
252A ILE* 1.3 63.4 + - + +
254A GLN* 3.3 7.6 + - - +
255A TYR* 3.0 22.5 + - - +
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Residues in contact with ILE 252 (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 THR* 3.8 29.4 - - + +
109A SER* 3.5 19.5 - - - +
110A PRO* 3.4 34.8 - - + -
113A MET* 3.9 11.2 - - - -
189A PHE* 6.4 0.2 - - + -
232A PHE* 4.0 21.5 - - + -
236A LEU* 4.4 1.3 - - + -
248A LEU* 3.0 38.7 + - + +
249A PRO 3.9 3.4 - - - +
251A VAL* 1.3 77.3 - - - +
253A ARG* 1.3 58.5 + - + +
255A TYR* 3.5 3.5 + - + +
256A GLY* 2.9 23.0 + - - -
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Residues in contact with ARG 253 (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 THR* 4.5 13.5 - - + +
110A PRO* 5.8 2.7 - - + -
249A PRO* 2.9 30.9 + - + +
250A GLN* 4.2 4.5 - - - +
252A ILE* 1.3 76.1 - - + +
254A GLN* 1.3 62.8 + - + +
256A GLY* 3.6 0.7 - - - +
257A ILE* 2.9 36.8 + - + +
114B ARG* 5.9 5.1 - - - +
115B TYR* 5.2 7.3 + - - -
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Residues in contact with GLN 254 (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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235A GLN* 5.3 4.9 + - - +
250A GLN* 3.0 47.2 + - - +
251A VAL* 3.9 6.6 - - - +
253A ARG* 1.3 75.7 - - + +
255A TYR* 1.3 65.5 + - - +
257A ILE* 3.2 13.9 - - + +
258A ALA* 3.0 25.6 + - - +
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Residues in contact with TYR 255 (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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105A ARG* 3.7 28.9 + - - -
185A ASP* 4.5 8.5 + - - -
189A PHE* 4.7 3.4 - + - -
219A TYR* 4.4 14.9 + - - -
220A PHE* 4.8 1.9 - - - -
228A LEU* 3.8 22.4 - - + -
229A ALA* 3.8 20.4 - - - +
232A PHE* 3.4 69.3 - + + -
251A VAL 3.0 11.9 + - - +
252A ILE* 3.8 3.4 - - + +
254A GLN* 1.3 75.7 - - - +
256A GLY* 1.3 54.1 + - - +
258A ALA* 4.6 4.5 - - + -
259A SER* 2.6 56.8 + - - -
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Residues in contact with GLY 256 (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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105A ARG* 6.3 0.2 - - - -
106A THR* 4.1 22.2 - - - -
252A ILE 2.9 16.4 + - - -
253A ARG 3.3 3.8 + - - -
254A GLN 3.1 0.4 - - - -
255A TYR* 1.3 79.8 - - - +
257A ILE* 1.3 56.6 + - - +
259A SER* 3.4 5.8 + - - -
260A GLY* 2.9 25.5 + - - -
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Residues in contact with ILE 257 (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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253A ARG* 2.9 18.5 + - + +
254A GLN* 3.2 20.4 - - + +
256A GLY* 1.3 74.3 - - - +
258A ALA* 1.3 67.7 + - + +
260A GLY* 3.3 2.3 + - - -
261A HIS* 2.9 49.2 + - + +
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Residues in contact with ALA 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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228A LEU* 3.6 24.0 - - + -
254A GLN 3.0 17.9 + - - +
255A TYR* 4.0 5.2 - - + +
257A ILE* 1.3 78.0 - - + +
259A SER* 1.3 60.1 + - - +
260A GLY 3.0 1.1 - - - -
261A HIS* 3.0 9.9 + - - +
262A ILE* 2.9 32.0 + - - +
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Residues in contact with SER 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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102A LEU* 5.4 3.8 - - - +
105A ARG* 4.6 7.1 + - - -
219A TYR* 3.1 31.0 - - - -
228A LEU* 4.7 2.1 - - - +
255A TYR* 2.6 45.8 + - - -
256A GLY* 3.4 7.3 + - - -
258A ALA* 1.3 77.0 - - - +
260A GLY* 1.3 58.6 + - - +
262A ILE* 3.7 5.6 - - - +
263A TRP* 2.9 29.6 + - - +
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Residues in contact with GLY 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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102A LEU* 5.6 5.4 - - - -
256A GLY 2.9 21.8 + - - -
257A ILE* 3.5 3.4 - - - -
258A ALA 3.0 0.2 - - - -
259A SER* 1.3 77.9 + - - +
261A HIS* 1.3 58.4 + - - +
263A TRP* 3.4 8.0 + - - +
264A ASN* 2.9 33.9 + - - +
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Residues in contact with HIS 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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257A ILE* 2.9 34.9 + - + +
258A ALA* 3.0 8.0 + - - +
260A GLY* 1.3 74.3 - - - +
262A ILE* 1.3 60.6 + - - +
264A ASN* 3.0 26.7 + - + +
265A GLN* 2.9 26.7 + - - +
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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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219A TYR* 3.6 25.6 - - + +
222A ASN* 4.5 7.9 - - - +
224A GLN* 3.8 31.2 - - + +
225A ALA* 3.8 15.0 - - + +
228A LEU* 3.9 21.3 - - + -
258A ALA 2.9 16.0 + - - +
259A SER* 3.7 7.2 - - - +
261A HIS* 1.3 73.1 - - - +
263A TRP* 1.3 65.0 + - - +
265A GLN* 3.1 13.7 + - - +
266A MET* 3.0 36.6 + - + +
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Residues in contact with TRP 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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94A ALA 5.3 1.6 - - - -
95A THR* 4.8 5.1 + - - +
98A VAL* 3.5 41.0 - - + +
99A GLU* 4.4 15.5 - - + +
102A LEU* 3.9 23.3 - - + -
215A VAL* 4.7 10.3 - - + -
218A TYR* 3.9 24.7 - + - -
219A TYR* 4.4 22.7 - + + -
259A SER 2.9 18.9 + - - +
260A GLY* 3.5 4.9 - - - +
262A ILE* 1.3 75.5 - - - +
264A ASN* 1.3 66.6 + - - +
266A MET* 2.9 10.6 + - + +
267A LYS* 2.9 51.3 + - + +
270A LEU* 4.1 15.7 - - + -
274A PHE* 4.0 22.9 - + - -
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Residues in contact with ASN 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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260A GLY 2.9 22.3 + - - +
261A HIS* 3.0 37.2 + - - +
263A TRP* 1.3 82.2 - - - +
265A GLN* 1.3 58.1 + - - +
267A LYS* 3.2 41.2 + - + +
268A MET* 4.4 8.0 - - - +
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Residues in contact with GLN 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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222A ASN* 3.4 26.2 + - - +
224A GLN* 4.1 15.0 + - - +
261A HIS 2.9 10.5 + - - +
262A ILE* 3.1 13.7 + - - +
264A ASN* 1.3 77.8 - - - +
266A MET* 1.3 68.8 + - - +
267A LYS 3.5 1.0 + - - -
268A MET* 3.9 15.7 + - - +
269A THR* 4.8 2.9 + - - -
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Residues in contact with MET 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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218A TYR* 2.7 77.5 + - + +
219A TYR* 3.7 23.3 - - - +
221A SER* 4.1 2.7 - - - +
222A ASN* 3.6 38.6 - - + +
262A ILE* 3.0 26.0 + - - +
263A TRP* 2.9 10.7 + - + +
265A GLN* 1.3 81.7 - - - +
267A LYS* 1.3 62.7 + - - +
268A MET 3.2 2.6 + - - -
269A THR* 3.7 9.7 + - - +
270A LEU* 3.9 0.5 - - - +
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Residues in contact with LYS 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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95A THR* 4.8 15.1 - - + +
99A GLU* 4.3 20.8 + - - -
263A TRP* 2.9 39.9 + - + +
264A ASN* 3.2 43.4 + - + +
265A GLN 3.4 0.2 - - - -
266A MET* 1.3 71.0 - - - +
268A MET* 1.3 76.4 + - - +
270A LEU* 3.3 28.5 - - + +
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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
------------------------------------------------------------
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