Contacts of the helix formed by residues 262 - 277 (chain I) in PDB entry 5GJQ
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 ASP 262 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H LYS* 4.2 8.5 + - - -
257I GLN* 2.2 57.9 + - + +
259I TYR* 2.9 43.1 + - - +
260I LEU 4.6 0.4 - - - -
261I GLY* 1.3 79.1 - - - +
263I GLY* 1.3 61.8 + - - +
264I PRO* 3.3 1.8 - - - -
265I LYS* 3.8 17.3 - - - +
266I LEU* 3.7 6.1 + - - +
304I GLU* 4.0 0.6 + - - -
229J ARG* 3.7 20.6 + - - +
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Residues in contact with GLY 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I LEU* 4.3 9.0 - - - +
257I GLN* 4.6 0.9 - - - +
262I ASP* 1.3 76.6 - - - +
264I PRO* 1.3 68.6 - - - +
265I LYS 3.6 0.4 - - - -
266I LEU* 4.3 4.0 - - - -
267I VAL* 3.2 28.4 + - - +
304I GLU* 4.7 2.4 + - - -
308I THR* 3.2 33.3 + - - +
311I GLU* 4.1 0.2 - - - +
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Residues in contact with PRO 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H SER* 3.9 26.7 - - - +
246H VAL 5.1 2.2 - - - +
261I GLY* 4.2 10.1 - - - -
262I ASP 3.5 8.5 - - - +
263I GLY* 1.3 96.7 - - - +
265I LYS* 1.3 54.9 + - - +
267I VAL 4.1 1.6 - - - -
268I ARG* 2.7 48.1 + - - +
304I GLU* 4.9 3.1 - - - +
307I ARG* 5.1 5.8 - - + -
308I THR* 3.9 12.3 - - - +
311I GLU* 3.5 27.8 - - + +
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Residues in contact with LYS 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H GLN* 5.3 10.2 - - - +
248H LYS* 5.3 14.3 - - - +
261I GLY 4.1 15.9 + - - +
262I ASP* 3.8 26.7 + - - +
263I GLY 3.6 0.2 - - - -
264I PRO* 1.3 77.6 - - - +
266I LEU* 1.3 55.2 + - - +
267I VAL 3.1 1.3 - - - -
268I ARG* 3.2 8.7 + - - +
269I GLU* 2.7 45.9 + - + +
229J ARG* 3.9 23.8 - - - +
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Residues in contact with LEU 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I LEU* 4.7 14.6 - - + -
174I MET* 5.0 3.6 - - - -
250I VAL* 6.1 1.6 - - + -
254I GLU* 3.1 24.0 - - + +
255I LEU* 4.0 22.0 - - + -
257I GLN* 2.8 42.6 - - - +
262I ASP 3.7 4.8 + - - +
263I GLY* 4.3 4.7 - - - +
265I LYS* 1.3 78.6 - - - +
267I VAL* 1.3 59.2 + - - +
269I GLU* 3.9 1.4 - - + +
270I LEU* 2.9 33.1 + - - +
229J ARG* 3.3 27.3 - - + +
230J MET* 4.8 15.7 - - + -
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Residues in contact with VAL 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I LEU* 3.2 29.2 - - + -
263I GLY 3.2 19.8 + - - +
264I PRO 4.1 0.2 - - - -
265I LYS 3.1 0.4 - - - -
266I LEU* 1.3 77.6 - - - +
268I ARG* 1.3 58.8 + - - +
270I LEU* 3.9 4.7 - - - +
271I PHE* 2.9 49.5 + - + +
308I THR 4.2 4.9 - - - +
311I GLU* 3.5 20.2 - - + -
312I LEU* 3.5 31.6 - - + -
315I GLN* 3.9 7.4 - - + -
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Residues in contact with ARG 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H THR* 5.9 1.2 + - - -
164H MET* 5.9 1.4 - - - +
241H ILE* 5.6 3.2 - - - +
243H SER* 3.4 13.3 + - - -
244H GLU* 3.1 55.3 + - - +
264I PRO* 2.7 28.8 + - - +
265I LYS* 3.2 10.6 + - - +
267I VAL* 1.3 75.3 - - - +
269I GLU* 1.3 57.6 + - - +
272I ARG* 2.4 58.1 + - + +
311I GLU* 3.1 19.0 + - - +
315I GLN* 3.6 12.7 - - + +
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Residues in contact with GLU 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I ASP* 4.8 2.6 - - - +
170I LEU* 2.7 37.1 - - + +
174I MET* 3.9 0.7 - - - -
265I LYS* 2.7 29.1 + - + +
266I LEU* 4.0 4.3 - - + +
268I ARG* 1.3 76.5 - - - +
270I LEU* 1.3 50.4 + - - +
272I ARG* 3.7 29.9 + - - +
273I VAL* 2.6 47.3 + - - +
229J ARG* 5.0 12.6 - - - +
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Residues in contact with LEU 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I MET* 3.1 22.3 - - + +
248I LEU* 3.2 41.8 - - + +
250I VAL* 2.8 49.8 - - + -
255I LEU* 5.1 1.3 - - + -
266I LEU 2.9 18.8 + - - +
267I VAL* 3.9 5.4 - - - +
269I GLU* 1.3 75.6 - - - +
271I PHE* 1.3 70.9 + - + +
273I VAL* 3.9 0.2 - - - +
274I ALA* 3.0 21.3 + - - +
282I VAL* 4.2 22.0 - - + -
284I ILE* 4.7 9.2 - - + -
312I LEU* 5.0 4.7 - - + -
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Residues in contact with PHE 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 2.9 33.2 + - + +
270I LEU* 1.3 86.1 - - + +
272I ARG* 1.3 59.3 - - - +
274I ALA* 3.2 3.2 + - - +
275I GLU 2.9 24.9 + - - -
282I VAL* 4.7 10.3 - - + -
284I ILE* 5.1 0.9 - - + -
312I LEU* 4.3 14.6 - - + -
315I GLN* 2.5 52.0 - - + +
316I LEU* 2.8 45.1 - - + -
322I ARG* 2.9 30.6 + - + -
325I VAL* 3.9 21.8 - - + -
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Residues in contact with ARG 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H MET* 4.7 17.4 - - - +
268I ARG* 2.4 49.1 + - - +
269I GLU* 3.7 29.6 + - - +
271I PHE* 1.3 70.0 - - - +
273I VAL* 1.3 60.0 + - + +
275I GLU* 3.5 6.8 + - - +
276I GLU* 3.0 49.1 + - - +
315I GLN* 4.0 0.9 + - - +
322I ARG* 3.8 3.1 - - - +
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Residues in contact with VAL 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ASP* 4.8 2.2 - - - +
170I LEU* 4.2 12.8 - - + -
171I VAL* 3.5 27.6 - - + -
174I MET* 4.1 10.1 - - + -
248I LEU* 4.0 15.9 - - + -
269I GLU* 2.6 38.5 + - - +
270I LEU 3.9 4.3 - - - +
272I ARG* 1.3 70.2 - - + +
274I ALA* 1.3 65.6 + - - +
276I GLU* 3.5 11.4 + - - +
277I HIS* 2.8 57.4 + - + +
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Residues in contact with ALA 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248I LEU* 3.1 26.2 - - + -
270I LEU 3.0 12.6 + - - +
271I PHE* 3.5 7.0 - - - +
273I VAL* 1.3 80.7 - - - +
275I GLU* 1.3 59.8 + - - +
276I GLU 3.4 0.3 + - - -
277I HIS* 3.7 1.4 + - - -
278I ALA 2.9 26.5 + - - +
280I SER* 3.0 14.5 + - - +
282I VAL* 3.4 20.6 - - + -
325I VAL* 4.2 9.2 - - + +
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Residues in contact with GLU 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I PHE 2.9 9.9 + - - +
272I ARG* 4.0 7.7 - - - +
274I ALA* 1.3 76.0 - - - +
276I GLU* 1.3 63.2 + - - +
278I ALA* 3.3 12.0 + - - -
320I ASP* 5.0 5.2 - - - +
321I SER 3.9 5.9 - - - +
322I ARG* 2.6 58.1 + - - +
324I ASP 6.0 0.9 - - - +
325I VAL* 4.3 5.8 - - + -
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Residues in contact with GLU 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I VAL* 4.8 6.2 - - - +
272I ARG* 3.0 38.7 + - + +
273I VAL* 3.6 21.7 - - - +
274I ALA 3.2 0.2 - - - -
275I GLU* 1.3 74.5 - - + +
277I HIS* 1.3 58.4 + - + +
278I ALA* 2.4 21.7 + - - +
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Residues in contact with HIS 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I VAL* 2.8 35.1 - - + +
175I LYS* 2.9 42.9 + - + -
246I THR* 3.6 26.3 - - + +
248I LEU* 4.9 3.1 - - + -
273I VAL* 2.8 39.9 + - + +
274I ALA 3.7 2.7 + - - +
275I GLU 3.7 0.2 - - - -
276I GLU* 1.3 78.5 + - + +
278I ALA* 1.3 69.5 + - - +
279I PRO 3.7 6.6 - - - +
280I SER* 4.8 0.4 - - - +
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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