Contacts of the helix formed by residues 249 - 267 (chain J) in PDB entry 6GYS
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 GLU 249 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227I ALA* 4.2 11.3 - - - +
81J LYS* 3.3 27.8 + - - -
210J GLN* 6.2 1.6 - - - +
214J ARG* 5.7 4.9 + - - +
245J PHE* 2.8 37.2 + - + +
246J PRO 3.9 0.4 - - - -
248J ASP* 1.3 83.8 - - + +
250J PRO* 1.3 60.8 - - - +
251J LEU 3.4 2.5 - - - -
252J LEU* 3.8 28.7 + - + +
253J ALA* 2.9 27.9 + - - +
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Residues in contact with PRO 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J TYR 4.3 0.7 - - - +
79J LYS* 3.3 44.6 - - + +
81J LYS* 3.7 21.1 - - + -
246J PRO 3.3 17.9 - - - +
247J TYR 3.4 13.9 - - - +
248J ASP 3.6 2.2 - - - +
249J GLU* 1.3 86.2 - - - +
251J LEU* 1.3 64.2 + - + +
253J ALA* 3.8 1.2 - - + +
254J ASN* 2.9 45.0 + - - +
307J ARG* 5.8 1.8 - - + -
503J LYS* 5.8 0.2 - - - +
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Residues in contact with LEU 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I MET 2.9 3.0 - - - +
227I ALA* 3.3 30.5 - - - +
229I PRO* 3.7 24.0 - - + -
262I HIS* 5.0 0.7 + - - -
266I ASN* 5.2 2.2 - - - +
79J LYS 4.8 0.7 - - - +
81J LYS* 3.7 44.2 - - + +
83J ARG* 4.2 20.0 - - + +
249J GLU 3.4 0.4 - - - -
250J PRO* 1.3 81.3 - - + +
252J LEU* 1.3 56.1 + - - +
254J ASN* 3.7 6.4 + - - +
255J SER* 2.7 33.3 + - - -
307J ARG* 4.2 28.9 - - + -
554J GLU* 6.0 0.9 - - - +
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Residues in contact with LEU 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I MET* 3.3 29.1 + - + +
227I ALA* 4.1 10.9 - - + +
217J LEU* 3.7 20.0 - - + -
221J LYS* 6.2 1.6 - - - +
245J PHE* 3.7 28.7 - - + -
249J GLU* 3.5 28.7 + - + +
250J PRO 3.3 0.2 - - - -
251J LEU* 1.3 78.9 - - - +
253J ALA* 1.3 58.3 - - - +
255J SER* 3.2 2.1 + - - -
256J LEU* 2.9 55.3 + - + +
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Residues in contact with ALA 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J TYR* 2.7 39.4 + - + +
245J PHE* 4.6 6.9 - - + +
246J PRO* 3.7 26.9 - - + +
249J GLU 2.9 19.3 + - - +
250J PRO* 3.3 4.5 + - + +
252J LEU* 1.3 75.4 - - - +
254J ASN* 1.3 60.7 + - - +
256J LEU* 4.7 0.2 - - - -
257J LEU* 2.8 18.9 + - - +
303J GLN* 4.0 4.3 - - - +
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Residues in contact with ASN 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I HIS* 3.7 11.4 - - + +
250J PRO* 2.9 29.6 + - - +
251J LEU* 4.1 3.5 - - - +
253J ALA* 1.3 75.3 - - - +
255J SER* 1.3 53.8 + - - +
257J LEU* 3.7 4.0 - - - +
258J THR* 2.6 38.1 + - - -
303J GLN* 2.9 26.5 + - - +
307J ARG* 3.3 44.1 + - - +
308J LYS* 3.3 22.4 - - + +
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Residues in contact with SER 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I PHE 4.8 0.3 + - - -
226I MET* 2.5 42.8 + - - -
259I GLN* 3.2 31.7 + - - +
262I HIS* 4.0 15.5 - - - -
251J LEU 2.7 9.4 + - - -
252J LEU 3.2 5.8 + - - -
253J ALA 3.2 0.6 - - - -
254J ASN* 1.3 76.1 - - - +
256J LEU* 1.3 61.0 + - - +
258J THR* 3.3 1.4 + - - -
259J GLN* 2.9 24.1 + - - +
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I MET* 3.6 24.7 - - + -
217J LEU* 4.5 15.5 - - + -
220J LEU* 4.8 7.9 - - + -
225J PHE* 4.0 22.9 - - + -
233J LEU* 4.2 15.7 - - + -
237J TYR* 3.6 28.3 - - + -
240J LEU* 6.4 0.9 - - + -
245J PHE* 6.4 1.8 - - + -
252J LEU* 2.9 48.2 + - + +
253J ALA* 4.7 0.2 - - - -
255J SER* 1.3 74.3 - - - +
257J LEU* 1.3 60.6 + - - +
259J GLN* 3.2 5.1 + - + +
260J CYS* 2.8 32.5 + - - -
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Residues in contact with LEU 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J TYR* 3.5 24.8 - - + +
253J ALA 2.8 19.3 + - - +
254J ASN 3.7 3.6 - - - +
256J LEU* 1.3 75.3 - - - +
258J THR* 1.3 59.9 + - - +
260J CYS* 3.1 5.5 + - - +
261J ILE* 2.9 37.9 + - + +
296J LEU* 3.8 23.6 - - + +
299J CYS* 3.3 34.3 - - + +
300J ASP* 3.9 2.7 - - + -
303J GLN* 3.3 21.3 - - - +
308J LYS* 3.7 27.8 - - + -
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Residues in contact with THR 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I THR* 3.7 19.2 - - + +
259I GLN* 4.1 3.1 - - - +
262I HIS* 3.0 30.3 + - + -
310I ILE* 4.4 3.8 - - + -
254J ASN 2.6 23.6 + - - -
255J SER 3.5 5.4 - - - -
257J LEU* 1.3 75.1 - - - +
259J GLN* 1.3 58.3 + - - +
261J ILE* 3.2 11.6 + - - +
262J HIS* 2.9 27.4 + - - +
308J LYS* 5.7 1.7 - - - +
310J ILE* 3.7 33.3 + - + +
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Residues in contact with GLN 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I MET* 3.7 15.5 - - + -
255I SER* 3.4 40.3 + - - +
258I THR* 3.7 11.7 - - - +
259I GLN* 3.0 23.6 - - - +
225J PHE* 4.0 11.4 - - + -
226J MET* 3.6 23.0 - - + +
229J PRO* 6.0 0.6 - - - +
233J LEU* 4.3 12.3 - - + -
255J SER 2.9 11.7 + - - +
256J LEU* 3.5 11.9 - - + +
257J LEU 3.2 0.2 - - - -
258J THR* 1.3 75.6 - - - +
260J CYS* 1.3 55.6 + - - +
262J HIS* 3.6 5.8 - - - +
263J THR* 2.8 38.8 + - - -
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Residues in contact with CYS 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J LEU* 4.4 6.5 - - - -
234J VAL* 3.7 34.7 - - + +
237J TYR* 3.6 36.1 - - - -
256J LEU 2.8 22.7 + - - -
257J LEU* 3.1 9.4 + - - +
259J GLN* 1.3 74.6 - - - +
261J ILE* 1.3 59.6 + - - +
263J THR* 4.4 0.2 - - - -
264J PHE* 2.9 35.9 + - - +
296J LEU* 3.8 18.8 - - + -
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Residues in contact with ILE 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I ILE* 3.8 17.7 - - + -
257J LEU* 2.9 28.1 + - + +
258J THR* 3.2 15.0 + - - +
260J CYS* 1.3 76.4 - - - +
262J HIS* 1.3 62.6 + - - +
264J PHE* 5.0 0.7 - - - -
265J LYS* 3.2 56.9 + - + +
296J LEU* 4.7 4.7 - - + -
300J ASP* 4.3 10.5 - - + +
310J ILE* 3.6 39.9 - - + +
311J ALA 4.9 0.7 - - - +
312J LEU* 3.6 24.7 - - + -
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Residues in contact with HIS 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I LEU 4.4 1.4 + - - -
254I ASN* 3.5 26.4 - - + +
255I SER* 3.1 34.6 + - - -
258I THR* 2.8 36.2 + - + +
307I ARG 4.0 2.6 + - - -
309I PRO* 3.3 40.5 - - + +
310I ILE* 4.1 4.9 + - + +
229J PRO* 5.1 5.1 - - + +
258J THR 2.9 16.6 + - - +
259J GLN* 3.6 7.4 - - - +
261J ILE* 1.3 75.8 - - - +
263J THR* 1.3 69.4 + - - +
266J ASN* 3.2 27.6 + - - +
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Residues in contact with THR 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J PRO* 3.5 25.1 - - + +
230J ASP 3.4 25.4 - - - +
231J ILE* 5.2 0.2 - - - -
233J LEU* 3.3 19.2 - - + +
234J VAL* 4.4 6.5 - - + -
259J GLN* 2.8 28.5 + - - -
260J CYS* 4.1 3.6 - - - -
262J HIS* 1.3 77.2 - - - +
264J PHE* 1.3 60.8 + - - +
266J ASN* 3.0 23.3 + - - +
267J PHE* 3.1 30.9 - - + -
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Residues in contact with PHE 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J ILE* 3.6 17.5 - - + -
234J VAL* 4.5 7.0 - - + -
260J CYS 2.9 19.4 + - - +
261J ILE 4.5 0.4 - - - +
263J THR* 1.3 77.5 - - - +
265J LYS* 1.3 67.3 + - + +
267J PHE* 3.4 15.7 + + - +
269J VAL* 3.5 51.4 - - + +
289J LEU* 3.2 49.1 - - + -
292J ILE* 3.9 17.3 - - + -
293J PHE* 3.9 26.2 - + + -
296J LEU* 3.8 20.0 - - + -
312J LEU* 5.7 0.4 - - + -
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Residues in contact with LYS 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I PRO 5.2 0.2 - - - +
309I PRO* 3.6 30.0 + - + +
310I ILE* 5.4 1.7 - - + +
261J ILE* 3.2 35.1 + - + +
264J PHE* 1.3 81.7 - - + +
266J ASN* 1.3 62.3 + - - +
267J PHE 3.2 1.8 - - - -
268J HIS* 3.2 22.0 + - - +
269J VAL 4.9 7.4 - - - +
293J PHE* 6.3 0.7 - - - -
311J ALA 4.2 10.1 + - - -
312J LEU* 3.6 33.3 - - + +
314J THR* 5.4 9.9 - - - +
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Residues in contact with ASN 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251I LEU* 4.7 11.9 - - - +
254I ASN* 6.2 0.2 - - - +
306I PRO 3.5 3.1 - - - +
307I ARG* 2.4 81.0 + - - +
309I PRO* 4.2 5.8 - - + +
554I GLU* 4.2 5.0 - - - +
229J PRO* 5.1 11.1 - - + +
262J HIS* 3.2 23.1 + - - +
263J THR* 3.0 15.7 + - + +
265J LYS* 1.3 77.6 - - - +
267J PHE* 1.3 58.8 + - + +
268J HIS* 3.1 7.5 - - - -
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Residues in contact with PHE 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553I ASP* 5.1 4.7 - - - +
554I GLU* 3.2 34.4 + - + -
555I MET* 5.4 4.4 + - - +
557I SER* 3.2 24.7 - - - -
558I LEU* 3.5 35.0 - - + -
229J PRO* 3.6 22.0 - - + -
230J ASP* 3.7 19.5 - - - -
231J ILE* 4.1 3.8 - - + -
263J THR* 3.1 43.6 + - + -
264J PHE* 3.7 12.6 - + - +
265J LYS 3.2 0.8 - - - -
266J ASN* 1.3 79.1 - - + +
268J HIS* 1.3 68.6 + - - +
269J VAL* 3.5 10.8 + - + +
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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
------------------------------------------------------------
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