Contacts of the helix formed by residues 258 - 272 (chain A) in PDB entry 4COO
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 GLY 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A VAL* 3.7 19.1 - - - -
256A GLY 3.1 2.8 - - - -
257A THR* 1.3 78.1 - - - +
259A GLY* 1.3 57.8 + - - +
260A THR 3.4 2.7 - - - -
261A ILE* 3.6 3.3 - - - +
262A THR* 2.7 38.1 + - - -
314A VAL 4.5 0.4 - - - -
315A LEU* 3.7 15.3 - - - -
1551A PLP 2.9 11.7 + - - -
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASN* 3.3 26.5 - - - -
229A PRO* 3.4 17.1 - - - +
232A HIS* 3.4 13.4 - - - -
257A THR* 3.0 10.4 + - - -
258A GLY* 1.3 76.9 - - - +
260A THR* 1.3 57.3 + - - +
263A GLY* 2.9 24.6 + - - -
314A VAL* 4.3 2.2 - - - +
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Residues in contact with THR 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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118A VAL* 3.9 11.2 - - + +
119A LYS* 5.9 0.2 - - - +
232A HIS* 3.2 29.6 + - + +
236A THR* 5.4 1.1 - - + -
253A ALA* 4.8 5.4 - - + -
254A SER 5.2 3.8 - - - +
259A GLY* 1.3 70.7 - - - +
261A ILE* 1.3 66.6 + - - +
264A ILE* 3.0 50.9 + - + +
373A ILE* 4.3 22.9 - - + -
1551A PLP 2.5 37.1 + - - -
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 5.1 3.1 - - + -
253A ALA* 3.9 23.0 - - + +
254A SER 5.2 1.3 + - - +
255A VAL* 4.2 16.2 - - + -
258A GLY* 3.6 12.3 - - - +
260A THR* 1.3 79.0 - - - +
262A THR* 1.3 61.4 + - - +
264A ILE* 4.1 3.1 - - - +
265A ALA* 2.9 35.2 + - - +
277A ILE* 3.8 24.2 - - + -
278A ILE 3.7 9.2 - - - +
279A GLY* 3.5 31.9 - - - -
315A LEU* 3.9 20.2 - - + -
316A ASP 5.6 0.2 - - - +
319A VAL* 5.3 0.2 - - - -
320A VAL* 3.9 15.9 - - + -
1551A PLP 5.0 1.0 + - - -
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Residues in contact with THR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 4.4 6.1 - - + -
258A GLY 2.7 23.0 + - - -
259A GLY 4.1 1.6 - - - -
261A ILE* 1.3 74.8 - - - +
263A GLY* 1.3 60.1 + - - +
265A ALA* 4.1 0.2 - - - +
266A ARG* 2.9 42.9 + - + +
314A VAL 3.4 17.5 + - - +
315A LEU* 3.5 6.9 - - - +
316A ASP* 3.0 43.0 + - + -
319A VAL* 4.4 7.2 - - - -
1552A EDO 3.6 11.7 - - - +
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.3 26.6 - - - +
232A HIS* 4.1 0.9 - - - -
233A TYR* 3.3 29.3 - - - -
259A GLY 2.9 13.2 + - - -
262A THR* 1.3 77.1 - - - +
264A ILE* 1.3 62.1 + - - +
267A LYS* 3.3 14.7 + - - +
1549A HEM 4.0 5.8 - - - -
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Residues in contact with ILE 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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232A HIS* 4.3 10.1 - - + -
236A THR* 4.0 12.1 - - + -
237A ALA* 3.9 22.0 - - + +
240A ILE* 4.0 8.3 - - + -
251A LEU* 3.9 22.2 - - + -
260A THR* 3.0 42.1 + - + +
261A ILE* 4.1 1.3 - - - +
263A GLY* 1.3 77.7 - - - +
265A ALA* 1.3 52.7 + - - +
267A LYS* 3.3 4.3 + - - +
268A LEU* 2.8 57.2 + - + +
373A ILE* 4.0 24.2 - - + -
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Residues in contact with ALA 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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251A LEU* 5.6 0.2 - - - +
261A ILE* 2.9 21.1 + - + +
264A ILE* 1.3 74.8 - - - +
266A ARG* 1.3 60.7 + - - +
268A LEU 4.4 0.2 - - - +
269A LYS* 2.8 38.0 + - - +
277A ILE* 3.7 29.2 - - + -
319A VAL* 3.6 34.5 - - + +
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Residues in contact with ARG 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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52A CYS* 3.3 19.6 + - - +
54A TRP* 3.3 51.8 + - + +
233A TYR* 3.8 17.3 - - + -
262A THR* 2.9 28.4 + - + +
265A ALA* 1.3 76.0 - - - +
267A LYS* 1.3 61.7 + - - +
269A LYS* 3.8 2.0 + - - +
270A GLU* 3.3 28.4 + - - +
316A ASP* 2.8 28.1 + - - -
319A VAL* 4.2 7.2 - - + -
1549A HEM 3.1 49.4 + - - +
1552A EDO 3.4 26.0 - - - -
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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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233A TYR* 2.8 66.0 + - + +
234A ASP* 4.4 3.8 + - - +
237A ALA* 3.6 28.9 - - + -
238A ASP* 3.0 30.4 + - - +
241A LEU* 4.3 9.9 - - + -
263A GLY 3.3 3.0 + - - +
264A ILE 3.3 3.3 + - - +
266A ARG* 1.3 76.8 - - - +
268A LEU* 1.3 60.1 + - - +
270A GLU* 3.1 9.5 + - - +
271A LYS* 2.9 46.1 + - + +
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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
----------------------------------------------------------
237A ALA* 4.7 7.4 - - + +
240A ILE* 5.0 3.8 - - + -
241A LEU* 3.7 38.8 - - + -
248A LEU* 4.2 14.6 - - + -
251A LEU* 4.2 13.9 - - + -
264A ILE* 2.8 43.8 + - + +
265A ALA 4.0 2.7 - - - +
267A LYS* 1.3 73.2 - - - +
269A LYS* 1.3 58.5 + - - +
271A LYS* 4.3 0.9 - - - +
272A CYS* 2.5 39.9 + - + +
275A CYS* 3.9 30.1 - - + +
277A ILE* 4.2 11.0 - - + -
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP* 5.2 1.8 - - + -
56A LEU* 3.7 36.0 - - + +
265A ALA 2.8 30.2 + - - +
266A ARG* 4.1 4.3 - - - +
268A LEU* 1.3 72.3 - - - +
270A GLU* 1.3 60.4 + - - +
272A CYS 4.8 0.2 - - - -
273A PRO* 3.6 34.0 + - + +
275A CYS 4.2 7.8 + - - +
277A ILE* 3.8 17.5 - - + -
318A THR 5.6 1.2 + - - -
319A VAL* 3.9 22.1 + - + +
321A ASP* 2.8 39.4 + - - -
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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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54A TRP* 2.8 28.3 + - - -
55A GLN 5.1 0.3 - - - +
56A LEU* 3.8 18.1 - - + +
57A GLY 5.3 2.9 + - - +
58A ARG 4.2 13.0 - - - +
60A ALA* 5.8 3.7 + - - +
233A TYR* 2.6 34.0 + - - -
266A ARG 3.3 13.1 + - - +
267A LYS* 3.1 10.8 + - - +
268A LEU 3.1 0.4 - - - -
269A LYS* 1.3 78.9 - - - +
271A LYS* 1.3 66.1 + - + +
273A PRO* 4.5 4.2 - - - +
1549A HEM 5.1 1.0 - - - +
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Residues in contact with LYS 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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238A ASP* 3.5 19.8 + - - -
241A LEU* 3.3 34.8 - - + +
246A GLY 5.5 1.6 - - - +
267A LYS* 2.9 35.1 + - + +
270A GLU* 1.3 79.5 - - + +
272A CYS* 1.3 60.0 + - - +
273A PRO* 3.6 6.8 - - - +
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Residues in contact with CYS 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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241A LEU* 4.2 16.8 - - + -
246A GLY 3.9 19.1 - - - +
247A LYS* 5.0 0.4 - - - -
248A LEU* 3.4 35.4 - - - -
268A LEU* 2.5 23.8 + - + +
269A LYS* 4.8 0.2 - - - -
271A LYS* 1.3 75.0 - - - +
273A PRO* 1.3 61.5 - - - +
274A GLY* 3.2 3.8 - - - -
275A CYS* 2.9 34.3 + - + +
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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