Contacts of the helix formed by residues 256 - 274 (chain A) in PDB entry 4N78
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 THR 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 4.2 0.2 - - - -
255A LEU* 1.3 81.9 - - + +
257A PRO* 1.3 76.2 - - - +
258A SER* 3.1 15.1 + - - -
259A GLU* 3.1 33.4 + - - +
260A LYS* 3.0 20.3 + - - +
402A SER* 3.5 0.7 - - - -
604A HIS* 5.2 1.6 - - + -
611A THR* 4.5 6.5 - - + +
614A GLN* 3.7 38.3 + - + +
615A CYS* 3.8 17.5 - - - -
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Residues in contact with PRO 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 1.3 87.4 - - - +
258A SER* 1.3 57.4 + - - +
260A LYS* 3.1 9.2 + - + +
261A HIS* 2.8 51.0 + - + +
402A SER* 3.2 31.4 - - - +
405A SER* 4.2 12.6 - - - -
406A ALA* 4.2 18.2 - - + +
409A MET* 6.0 3.6 - - + -
614A GLN 3.7 14.4 - - - +
615A CYS* 4.2 3.4 - - - -
617A ASP 6.1 1.1 - - - +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 3.1 13.5 + - - -
257A PRO* 1.3 80.6 - - - +
259A GLU* 1.3 60.9 + - - +
261A HIS* 4.0 6.8 - - - +
262A MET* 2.9 33.9 + - - +
265A LYS* 5.1 2.5 + - - +
614A GLN* 5.5 1.7 + - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.8 13.1 - - + +
255A LEU* 2.8 28.9 + - - +
256A THR* 3.1 30.0 + - - +
258A SER* 1.3 80.7 + - - +
260A LYS* 1.3 66.3 + - - +
262A MET* 3.4 13.6 + - - +
263A LEU* 3.4 19.2 + - - +
604A HIS* 2.6 31.4 + - - -
614A GLN* 5.5 1.2 - - - +
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 3.9 27.1 - - + -
254A TYR* 3.4 51.2 + - + -
256A THR 3.0 7.8 + - - +
257A PRO* 3.3 9.4 - - + +
259A GLU* 1.3 78.3 - - - +
261A HIS* 1.3 66.4 + - + +
263A LEU* 3.5 15.7 + - - +
264A LEU* 3.8 9.0 + - - +
302A LEU* 4.1 7.2 - - - +
406A ALA* 4.3 14.5 - - + +
410A GLU* 2.9 33.6 + - - +
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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
----------------------------------------------------------
257A PRO* 2.8 34.7 + - + +
258A SER* 4.0 6.5 + - - +
260A LYS* 1.3 84.8 - - + +
262A MET* 1.3 64.4 + - - +
264A LEU* 3.3 6.0 + - - +
265A LYS* 3.1 38.8 + - - +
302A LEU* 4.3 3.1 - - + -
305A VAL* 3.7 29.9 - - + +
306A PRO* 3.5 29.3 - - + +
406A ALA* 4.7 2.9 - - - +
409A MET* 4.9 8.7 - - + -
410A GLU* 3.0 38.6 + - + +
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Residues in contact with MET 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 6.1 1.6 - - + -
163A LYS* 4.2 35.7 - - + -
166A ASN* 3.5 45.8 - - - +
258A SER* 2.9 19.5 + - - +
259A GLU* 3.6 9.4 - - - +
260A LYS 3.3 0.4 - - - -
261A HIS* 1.3 75.7 - - - +
263A LEU* 1.3 67.5 + - + +
265A LYS* 3.3 15.4 + - - +
266A VAL* 2.9 37.6 + - + +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.4 7.0 - - + -
245A CYS* 3.7 32.1 - - + +
248A TYR* 3.8 28.0 - - + -
249A TYR* 3.6 33.0 - - + +
253A MET 4.5 0.7 - - - +
254A TYR* 3.7 28.9 - - + -
259A GLU 3.4 14.8 + - - +
260A LYS 3.6 6.1 - - - +
261A HIS 3.2 0.6 - - - -
262A MET* 1.3 79.9 - - + +
264A LEU* 1.3 61.4 + - - +
266A VAL* 3.3 3.2 + - - +
267A MET* 3.0 32.7 + - + +
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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
----------------------------------------------------------
249A TYR* 3.6 40.2 - - + +
260A LYS 3.8 6.7 + - - +
261A HIS* 3.3 8.0 + - + +
262A MET 3.3 0.4 - - - -
263A LEU* 1.3 75.7 - - - +
265A LYS* 1.3 58.5 + - - +
267A MET* 3.2 17.7 + - - +
268A GLY* 3.0 24.6 + - - -
298A TYR* 3.9 22.0 - - + -
299A PHE* 3.7 14.3 - - + -
302A LEU* 3.6 33.9 - - + -
305A VAL* 4.3 7.2 - - + -
315A LEU* 3.8 28.0 - - + +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 3.5 28.7 + - - +
258A SER* 5.1 2.0 + - - +
261A HIS* 3.1 35.9 + - - +
262A MET* 3.3 22.9 + - - +
264A LEU* 1.3 75.8 - - - +
266A VAL* 1.3 60.7 + - - +
268A GLY 4.6 0.2 - - - +
269A PHE* 3.2 26.5 + - - +
305A VAL* 3.8 14.8 - - + -
306A PRO 3.1 28.4 + - - +
307A LEU* 4.1 16.5 + - + -
313A ILE* 3.9 18.4 - - + -
315A LEU* 4.2 7.2 - - + -
318A TYR* 4.0 9.0 + - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY* 3.5 27.6 - - - +
163A LYS* 5.6 0.2 - - + -
165A ILE* 3.9 15.8 - - + +
166A ASN* 4.7 2.5 - - + -
241A ILE* 3.7 25.1 - - + +
242A VAL* 4.4 2.6 - - + +
245A CYS* 3.5 24.9 - - - -
262A MET* 2.9 37.0 + - + +
263A LEU 3.6 4.5 - - - +
265A LYS* 1.3 75.8 - - - +
267A MET* 1.3 56.2 + - - +
270A GLY* 2.8 33.4 + - - -
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Residues in contact with MET 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 4.3 12.4 - - - +
245A CYS* 3.2 42.2 - - + +
246A VAL* 3.5 19.7 - - + +
249A TYR* 3.6 21.1 - - + -
263A LEU 3.0 20.4 + - - +
264A LEU* 3.2 17.7 + - + +
266A VAL* 1.3 76.6 - - - +
268A GLY* 1.3 63.3 + - - +
270A GLY* 3.7 0.2 - - - -
271A LEU* 3.0 31.2 + - - +
295A ILE* 4.4 15.3 - - + -
298A TYR* 3.9 21.1 - - + -
299A PHE* 4.2 11.7 - - + -
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 3.0 11.8 + - - -
266A VAL 3.2 0.2 - - - -
267A MET* 1.3 78.6 - - - +
269A PHE* 1.3 61.6 + - - +
270A GLY 3.2 0.2 + - - -
271A LEU* 3.3 4.9 + - - +
272A TYR 3.1 17.3 + - - -
299A PHE* 3.7 18.1 - - - -
318A TYR* 3.3 34.1 - - - +
319A ILE* 5.6 0.2 - - - -
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Residues in contact with PHE 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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165A ILE* 3.0 44.9 - - + -
166A ASN* 4.4 1.3 - - - +
168A PHE* 4.3 0.9 - - + -
169A ALA* 3.7 24.7 - - + -
221A THR* 4.0 28.9 - - + -
224A LEU* 4.2 11.0 - - + -
265A LYS 3.2 17.0 + - - +
266A VAL 4.5 0.7 - - - +
268A GLY* 1.3 73.4 - - - +
270A GLY* 1.3 60.9 + - - +
272A TYR* 3.7 26.2 - + - -
273A LEU* 3.0 43.3 + - + +
318A TYR* 3.4 29.7 - + + +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 4.1 12.7 - - - +
238A LEU* 4.3 4.9 - - - +
242A VAL* 4.0 10.1 - - - -
266A VAL 2.8 20.5 + - - -
267A MET 3.7 0.7 - - - -
269A PHE* 1.3 74.0 - - - +
271A LEU* 1.3 64.9 + - - +
273A LEU* 3.1 7.5 + - - +
274A MET* 2.9 32.8 + - - +
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Residues in contact with LEU 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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242A VAL* 4.3 10.1 - - + +
267A MET 3.0 19.2 + - - +
268A GLY* 3.8 4.3 - - - +
270A GLY* 1.3 73.8 - - - +
272A TYR* 1.3 62.5 + - - +
274A MET* 3.1 12.5 + - - -
275A ASP* 3.1 20.5 + - - +
281A ILE* 3.4 22.0 - - + +
290A ILE* 4.1 15.0 - - + -
292A LEU* 3.9 28.7 - - + -
295A ILE* 3.6 42.4 - - + -
319A ILE* 4.0 23.1 - - + -
322A SER* 5.7 0.7 - - - -
332A TRP* 4.2 2.5 - - + -
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A THR* 4.1 23.0 - - + +
225A GLN* 3.8 28.4 + - - -
268A GLY 3.1 13.4 + - - +
269A PHE* 3.5 30.5 - + + +
271A LEU* 1.3 77.3 - - - +
273A LEU* 1.3 65.2 + - + +
275A ASP* 3.2 23.0 + - - +
318A TYR* 3.7 22.6 + + + +
321A THR* 3.3 51.1 + - + -
322A SER* 4.1 8.1 - - - -
323A ALA 5.5 0.7 - - - -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 4.2 20.2 - - + -
221A THR 4.9 1.3 - - - +
224A LEU* 3.7 29.6 - - + -
225A GLN* 3.6 34.7 + - + +
228A LEU* 4.2 13.6 - - + +
229A GLU* 5.1 1.9 - - - +
234A TYR* 2.8 24.6 + - - -
238A LEU* 3.8 15.0 - - + -
269A PHE* 3.0 49.9 + - + +
270A GLY* 3.6 4.0 - - - +
272A TYR* 1.3 75.4 - - + +
274A MET* 1.3 56.2 + - - +
275A ASP 3.1 9.1 + - - -
276A GLY 4.5 0.2 + - - -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 4.1 6.7 - - - -
235A GLU* 3.7 17.5 - - + +
238A LEU* 3.5 37.0 - - + +
239A ALA* 3.8 18.6 - - + -
242A VAL* 4.0 13.2 - - - -
270A GLY 2.9 21.2 + - - +
271A LEU* 3.1 10.7 + - - +
273A LEU* 1.3 75.7 - - - +
275A ASP* 1.3 57.5 + - - +
276A GLY 3.8 1.1 - - - -
279A SER* 2.8 32.8 + - - +
280A ASN 3.7 0.2 + - - -
281A ILE* 3.6 12.4 - - + +
284A LEU* 3.5 25.4 - - + -
290A ILE* 4.3 18.2 - - + -
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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