Contacts of the helix formed by residues 254 - 272 (chain A) in PDB entry 1GC5
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 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A LYS 4.3 0.9 - - - -
247A GLU 3.2 17.9 - - - +
248A TYR* 3.5 22.9 - - + -
249A TYR* 4.3 9.5 - - - -
252A GLY 4.6 4.9 - - - +
253A THR* 1.3 82.9 - - - +
255A TYR* 1.3 71.1 + - - +
256A LYS* 3.7 19.0 + - - +
257A ASP* 3.2 28.0 + - - +
258A VAL* 4.2 4.2 + - - +
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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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245A LEU* 4.2 19.0 - - + +
246A LYS 3.1 22.3 + - - +
247A GLU* 3.8 37.7 - - + -
248A TYR* 6.4 0.2 - + - -
249A TYR* 4.9 1.6 - - - -
254A THR* 1.3 76.5 - - - +
256A LYS* 1.3 93.5 + - + +
258A VAL* 2.9 17.0 + - - +
259A LEU* 3.1 44.1 + - + +
287A ARG* 4.5 12.9 + - + +
288A VAL* 4.0 16.8 - - + -
291A ALA* 3.5 18.7 - - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 3.1 12.3 - - - +
255A TYR* 1.3 115.4 + - + +
257A ASP* 1.3 63.4 + - - +
259A LEU* 3.9 23.4 - - - +
260A ASP* 2.9 60.7 + - - +
291A ALA* 5.0 3.6 - - - +
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Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.7 27.4 - - - +
254A THR* 3.2 23.9 + - - +
255A TYR 3.1 0.4 + - - -
256A LYS* 1.3 79.3 - - - +
258A VAL* 1.3 66.6 + - + +
260A ASP* 3.8 6.7 - - - +
261A ARG* 3.5 39.5 + - - +
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Residues in contact with VAL 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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216A ARG 3.9 13.5 - - - +
217A VAL* 3.9 30.7 - - + +
219A MET* 4.1 11.7 - - + -
242A LEU* 4.7 0.7 - - + -
245A LEU* 3.7 33.0 - - + -
249A TYR* 6.0 1.8 - - + -
254A THR 4.6 7.0 - - - +
255A TYR 2.9 7.8 + - - +
257A ASP* 1.3 76.1 - - + +
259A LEU* 1.3 57.4 + - - +
260A ASP 3.1 2.0 - - - -
261A ARG* 2.7 39.5 + - - +
262A VAL* 3.0 16.2 + - + +
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Residues in contact with LEU 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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242A LEU* 4.3 9.9 - - + -
245A LEU* 3.8 20.0 - - + -
255A TYR* 3.1 47.3 + - + +
256A LYS* 3.9 18.2 - - - +
258A VAL* 1.3 77.9 - - - +
260A ASP* 1.3 57.6 + - - +
262A VAL* 3.6 5.9 - - + +
263A GLU* 2.8 33.3 + - - +
288A VAL* 5.0 2.5 - - + +
291A ALA* 3.5 23.3 - - + -
292A LEU* 3.9 22.9 - - + -
295A LEU* 4.0 17.1 - - + +
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Residues in contact with ASP 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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256A LYS* 2.9 52.3 + - - +
257A ASP* 3.8 6.9 - - - +
259A LEU* 1.3 77.6 - - - +
261A ARG* 1.3 62.2 + - - +
263A GLU* 3.6 5.8 + - - +
264A SER* 3.4 19.6 + - - -
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Residues in contact with ARG 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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216A ARG 5.8 0.2 + - - -
217A VAL 4.9 1.4 + - - -
219A MET* 3.9 23.0 - - + +
224A ARG* 3.2 52.2 - - + +
257A ASP* 3.5 36.5 + - - +
258A VAL* 2.7 33.9 + - - +
260A ASP* 1.3 75.5 - - - +
262A VAL* 1.3 59.4 + - - +
264A SER* 2.8 23.5 + - - +
265A HIS* 3.4 18.3 + - + +
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Residues in contact with VAL 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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37A TYR* 3.8 36.6 - - + +
219A MET* 3.9 12.3 - - + -
239A ILE* 5.0 4.7 - - + -
242A LEU* 4.2 25.6 - - + -
258A VAL* 3.0 24.0 + - + +
259A LEU* 3.2 11.0 + - + +
261A ARG* 1.3 75.0 - - - +
263A GLU* 1.3 64.0 + - - +
265A HIS* 3.0 13.4 + - - +
266A LEU* 3.1 27.7 + - + +
295A LEU* 4.5 9.4 - - + -
299A PHE* 5.7 1.3 - - + -
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Residues in contact with GLU 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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259A LEU 2.8 21.6 + - - +
260A ASP* 3.9 7.0 - - - +
261A ARG 3.4 0.2 - - - -
262A VAL* 1.3 74.0 - - - +
264A SER* 1.3 59.5 + - - +
266A LEU* 3.4 10.3 + - - +
267A ASN* 2.8 49.5 + - - +
295A LEU* 3.4 26.0 - - + +
298A LYS* 2.7 36.8 + - + -
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Residues in contact with SER 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 ASP 3.4 10.5 + - - -
261A ARG* 2.8 20.5 + - - +
263A GLU* 1.3 76.9 - - - +
265A HIS* 1.3 67.1 + - - +
267A ASN* 3.8 12.9 - - - +
268A ILE* 3.1 30.9 + - - +
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Residues in contact with HIS 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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37A TYR* 2.9 30.7 + + - +
219A MET* 4.0 24.0 - - - -
223A PHE* 2.9 30.6 + - + -
224A ARG* 4.7 3.6 + - - -
227A PHE* 3.3 52.1 - + + -
239A ILE* 6.1 1.6 - - + -
261A ARG* 3.4 15.3 + - - +
262A VAL* 3.0 9.5 + - - +
264A SER* 1.3 85.7 + - - +
266A LEU* 1.3 61.1 + - + +
267A ASN 3.2 0.4 - - - -
268A ILE* 3.1 4.1 + - + -
269A LEU* 2.9 28.7 + - + +
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Residues in contact with LEU 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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239A ILE* 4.7 5.2 - - + -
262A VAL* 3.1 21.9 + - + +
263A GLU* 3.7 7.2 - - + +
264A SER 3.4 0.2 - - - -
265A HIS* 1.3 78.3 - - + +
267A ASN* 1.3 57.4 + - - +
269A LEU* 3.3 18.7 + - + +
270A ASN* 2.8 36.0 + - - -
276A SER* 4.7 2.5 - - - +
295A LEU* 3.5 32.1 - - + -
298A LYS* 4.2 25.1 - - + +
299A PHE* 3.3 50.7 - - + -
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Residues in contact with ASN 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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263A GLU* 2.8 33.9 + - - +
264A SER* 3.8 10.8 - - - +
265A HIS 3.2 0.6 - - - -
266A LEU* 1.3 77.3 - - - +
268A ILE* 1.3 57.5 + - + +
270A ASN* 3.6 8.1 + - - +
271A ARG* 2.8 33.0 + - - +
298A LYS* 2.8 32.7 + - - +
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Residues in contact with ILE 268 (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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227A PHE* 3.6 26.9 - - + -
228A GLU* 3.9 28.3 - - + +
231A THR* 4.0 10.5 - - - +
264A SER* 3.1 18.6 - - - +
265A HIS* 3.1 8.4 + - + +
267A ASN* 1.3 75.6 - - + +
269A LEU* 1.3 67.0 + - - +
271A ARG* 3.2 24.5 + - - +
272A TYR* 3.0 50.9 + - + -
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Residues in contact with LEU 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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34A LEU* 4.4 5.2 - - + -
227A PHE* 4.1 14.4 - - + -
231A THR* 3.6 25.4 - - + +
234A VAL* 5.1 1.1 - - + -
237A ALA* 4.0 23.1 - - + -
239A ILE* 4.9 9.2 - - + -
265A HIS* 2.9 19.3 + - + +
266A LEU* 3.5 21.1 - - + +
268A ILE* 1.3 78.2 - - - +
270A ASN* 1.3 61.6 + - - +
272A TYR* 3.1 3.3 + - - -
273A ASN 3.0 4.2 + - - -
274A VAL* 2.8 56.6 + - + +
276A SER* 4.2 15.5 - - - +
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Residues in contact with ASN 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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266A LEU 2.8 23.8 + - - +
267A ASN* 3.6 9.8 + - - +
269A LEU* 1.3 78.2 - - - +
271A ARG* 1.3 55.4 + - - +
273A ASN* 2.6 33.9 + - - +
274A VAL 4.8 6.4 - - - +
276A SER* 5.3 1.6 + - - -
298A LYS* 3.5 40.7 + - - +
300A THR* 5.6 1.9 + - - -
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Residues in contact with ARG 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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228A GLU* 3.3 37.8 + - - -
267A ASN* 2.8 20.3 + - - +
268A ILE* 3.2 29.1 + - - +
270A ASN* 1.3 75.9 - - - +
272A TYR* 1.3 75.6 + - + +
273A ASN* 3.3 5.9 + - - -
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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
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228A GLU* 2.5 41.0 + - + +
231A THR* 3.8 21.1 - - + +
232A ARG* 2.6 50.0 + - + -
268A ILE* 3.0 31.1 + - + +
269A LEU 3.1 3.1 + - - +
270A ASN 3.0 0.8 - - - -
271A ARG* 1.3 98.1 + - + +
273A ASN* 1.3 74.3 + - - +
274A VAL* 3.2 7.3 + - + +
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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