Contacts of the helix formed by residues 257 - 275 (chain A) in PDB entry 4ILG
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 PRO 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.8 0.9 - - + -
206A ASN* 3.5 22.4 - - - +
210A LEU* 4.1 20.9 - - + -
255A THR* 4.5 1.1 - - + +
256A VAL* 1.3 89.7 - - + +
258A LYS* 1.3 66.1 + - - +
259A HIS* 3.2 26.0 - - + +
260A MET* 3.0 18.7 + - + +
261A LEU* 3.3 8.3 + - - +
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL 3.2 6.1 + - - -
257A PRO* 1.3 71.0 - - - +
259A HIS* 1.3 63.4 + - - +
261A LEU* 3.2 11.5 + - + +
262A ASP* 3.2 48.5 + - - +
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 3.0 33.0 + - - -
221A PHE* 5.0 0.6 - + - -
257A PRO* 3.1 25.0 + - + +
258A LYS* 1.3 79.3 - - - +
260A MET* 1.3 66.9 + - + +
262A ASP* 4.0 6.0 + - - +
263A LYS* 3.6 20.8 + - - +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 5.0 2.2 - - + -
210A LEU* 3.7 29.8 - - + -
217A SER* 3.4 30.5 - - - -
220A TYR* 3.5 39.7 - - + -
221A PHE* 3.3 25.7 - - + -
250A ILE* 3.8 18.4 - - + -
256A VAL* 4.1 11.0 - - + -
257A PRO* 3.0 17.1 + - + +
259A HIS* 1.3 88.0 - - + +
261A LEU* 1.3 66.3 + - - +
263A LYS 3.2 1.4 + - - -
264A LEU* 3.1 20.5 + - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 4.4 9.6 - - + -
256A VAL* 3.9 28.9 - - + +
257A PRO 3.3 4.1 + - - +
258A LYS* 3.2 15.2 + - + +
260A MET* 1.3 79.7 - - - +
262A ASP* 1.3 68.7 + - - +
264A LEU* 3.3 22.7 + - + +
265A ASP* 4.1 3.5 + - - +
298A GLN* 3.5 39.3 - - + +
301A SER* 3.7 39.6 - - - +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 3.2 51.5 + - - +
259A HIS* 4.4 5.9 - - - +
260A MET 3.3 0.2 - - - -
261A LEU* 1.3 82.9 - - - +
263A LYS* 1.3 59.5 + - - +
264A LEU 3.4 0.2 - - - -
265A ASP* 4.4 7.3 + - - +
266A GLU* 4.6 8.8 + - - +
301A SER* 5.7 1.0 + - - -
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 3.1 32.8 + - - -
120A PHE* 3.7 24.0 - - + -
221A PHE* 3.9 12.3 - - + -
259A HIS 3.6 16.0 + - - +
260A MET 3.2 5.2 + - - +
262A ASP* 1.3 79.3 - - - +
264A LEU* 1.3 63.6 + - - +
265A ASP 3.4 0.2 - - - -
266A GLU* 3.3 38.8 + - - +
267A ILE* 3.2 36.7 + - + +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 4.2 21.3 - - + -
224A LEU* 4.5 12.3 - - + -
247A ILE* 5.0 5.4 - - + +
250A ILE* 3.7 36.3 - - + -
251A CYS* 4.3 16.8 - - - -
260A MET 3.1 11.3 + - - +
261A LEU* 3.3 17.6 + - + +
263A LYS* 1.3 78.0 - - - +
265A ASP* 1.3 62.9 + - - +
267A ILE* 3.1 15.4 + - + +
268A LEU* 3.1 42.2 + - + +
301A SER* 6.3 0.2 - - - -
302A LEU* 4.2 9.9 - - + -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 4.1 3.4 + - - +
262A ASP 4.8 6.5 - - - +
263A LYS 3.4 0.6 - - - -
264A LEU* 1.3 77.0 - - - +
266A GLU* 1.3 58.4 + - - +
269A TYR* 2.9 29.0 + - - +
301A SER 3.2 22.8 - - - +
302A LEU* 3.3 17.2 - - - +
303A HIS* 3.4 5.9 + - - +
304A ASN* 3.0 36.3 + - - +
305A THR* 2.9 38.1 + - - -
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 5.6 1.7 + - - -
119A GLU* 5.1 0.3 - - - +
262A ASP 4.6 7.7 + - - +
263A LYS* 3.3 45.1 + - + +
265A ASP* 1.3 78.4 - - - +
267A ILE* 1.3 64.5 + - - +
269A TYR* 3.2 15.4 + - - +
270A TYR* 3.3 42.5 + - + +
304A ASN* 5.6 4.2 - - - +
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN 5.4 2.8 - - - +
120A PHE* 3.8 20.9 - - + -
221A PHE* 3.5 43.5 - - + -
224A LEU* 4.0 16.4 - - + -
225A GLN* 4.0 20.3 + - + +
263A LYS* 3.2 23.3 + - + +
264A LEU* 3.1 10.8 + - + +
266A GLU* 1.3 81.5 - - + +
268A LEU* 1.3 62.4 - - + +
270A TYR* 3.6 7.0 + - - +
271A GLN* 3.3 40.0 + - - +
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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
----------------------------------------------------------
224A LEU* 4.6 5.2 - - + -
243A TRP* 4.1 2.2 - - + +
247A ILE* 3.6 44.4 - - + -
264A LEU* 3.1 33.0 + - + +
267A ILE* 1.3 73.7 - - - +
269A TYR* 1.3 60.1 + - - +
271A GLN* 3.0 22.9 + - - +
272A ILE* 2.9 35.2 + - - +
289A TRP* 4.2 17.5 - - + -
302A LEU* 3.8 23.6 - - + -
305A THR* 3.2 18.2 - - + +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP 2.9 19.8 + - - +
266A GLU* 3.2 6.7 + - - +
268A LEU* 1.3 76.8 - - - +
270A TYR* 1.3 83.0 + + - +
272A ILE* 3.8 1.6 - - - +
273A LYS* 2.8 64.7 + - + +
304A ASN* 3.9 28.9 - - + +
305A THR* 3.2 9.6 + - - +
308A ILE* 3.6 37.5 - - + +
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Residues in contact with TYR 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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113A THR* 5.5 8.6 - - + +
116A ASN* 3.4 54.2 + - + +
117A LEU* 3.5 17.5 - - + +
266A GLU* 3.3 42.7 + - + +
267A ILE* 3.9 6.5 - - - +
269A TYR* 1.3 103.6 - + - +
271A GLN* 1.3 61.9 + - - +
273A LYS* 3.8 17.2 - - + +
274A THR* 3.2 24.6 + - - -
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Residues in contact with GLN 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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117A LEU* 3.9 15.0 + - + -
224A LEU* 3.8 16.2 - - - +
225A GLN* 3.8 16.5 + - - +
228A PHE* 3.3 55.5 - - + +
243A TRP* 2.8 27.7 + - + -
267A ILE* 3.3 21.7 + - - +
268A LEU* 3.0 22.5 + - - +
270A TYR* 1.3 73.2 - - - +
272A ILE* 1.3 66.5 + - - +
274A THR* 3.2 19.2 - - - +
275A LEU* 3.3 6.4 + - - +
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Residues in contact with ILE 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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243A TRP* 4.3 8.5 - - + -
268A LEU 2.9 21.8 + - - +
269A TYR 3.8 3.1 - - - +
271A GLN* 1.3 76.0 - - - +
273A LYS* 1.3 62.2 + - - +
274A THR 3.3 0.5 + - - -
275A LEU* 3.3 14.6 + - + +
284A LEU* 4.3 10.3 - - + -
289A TRP* 3.9 17.3 - - + -
305A THR* 4.4 16.2 - - + -
308A ILE* 3.7 26.9 - - + -
309A MET* 3.6 35.2 - - + +
312A LYS* 3.1 18.2 + - - -
313A TYR* 4.0 19.7 + - + -
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Residues in contact with LYS 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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113A THR* 5.7 5.4 + - + +
269A TYR* 2.8 51.0 + - + +
270A TYR* 3.8 19.1 - - + +
272A ILE* 1.3 72.8 - - - +
274A THR* 1.3 62.4 + - - +
275A LEU 3.9 0.3 - - - +
308A ILE* 3.6 22.2 - - + +
312A LYS* 3.3 18.9 - - - +
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Residues in contact with THR 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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19A GLN* 5.2 8.3 - - - +
113A THR* 4.6 11.3 - - - +
117A LEU* 4.1 19.7 - - + +
228A PHE* 4.1 8.5 - - + -
232A MET* 3.7 26.6 - - + +
270A TYR 3.2 13.8 + - - +
271A GLN* 3.2 18.8 - - - +
273A LYS* 1.3 78.6 - - - +
275A LEU* 1.3 67.0 + - - +
276A PRO* 3.5 5.7 - - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.9 17.9 - - + -
232A MET* 3.8 20.2 - - + -
271A GLN 3.3 13.0 + - - +
272A ILE* 3.3 12.4 + - + +
273A LYS 3.9 0.5 - - - +
274A THR* 1.3 82.3 - - - +
276A PRO* 1.3 70.8 - - + +
277A GLU* 4.4 0.9 - - - +
280A SER* 4.1 16.6 - - - -
283A LEU* 3.8 28.7 - - + -
284A LEU* 4.0 31.6 - - + -
312A LYS* 2.5 28.4 + - - -
313A TYR* 3.4 13.0 - - + +
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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
------------------------------------------------------------
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