Contacts of the helix formed by residues 235 - 246 (chain O) in PDB entry 6RQT
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 235 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A THR* 5.6 3.6 - - + -
564A PRO 4.8 2.3 - - - +
565A SER 4.9 0.3 - - - -
566A SER* 3.8 32.4 + - - -
195O ALA* 5.7 2.3 - - - +
231O SER 3.6 21.5 - - - +
232O LEU* 3.1 12.0 + - - +
234O ILE* 1.3 79.4 - - + +
236O LYS* 1.3 76.6 + - + +
237O ILE 3.3 0.2 - - - -
238O ILE* 3.3 31.7 + - - +
239O SER* 4.0 2.8 + - - -
371O HIS* 3.9 27.7 + - + +
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Residues in contact with LYS 236 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O PHE* 3.5 53.8 - - + -
232O LEU* 3.2 37.5 + - + +
233O LEU* 4.1 10.0 - - + -
234O ILE 3.4 0.6 - - - -
235O GLU* 1.3 89.8 + - + +
237O ILE* 1.3 63.2 + - - +
238O ILE 3.2 0.4 - - - -
239O SER* 3.9 21.5 + - - +
240O ILE* 4.3 13.3 + - - +
335O ILE* 5.8 3.5 - - - +
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Residues in contact with ILE 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233O LEU 3.3 21.8 - - - +
234O ILE* 4.2 11.0 - - + +
235O GLU 3.3 0.8 - - - -
236O LYS* 1.3 79.4 - - - +
238O ILE* 1.3 62.4 + - - +
239O SER 3.5 0.2 + - - -
240O ILE* 3.9 3.5 + - - +
241O ASP* 3.3 18.4 + - - +
335O ILE* 5.9 9.0 - - + -
336O LEU* 6.4 1.3 - - + -
380O SER* 4.2 10.8 - - - +
381O ILE* 3.7 37.0 - - + -
384O ILE* 4.0 30.3 - - + -
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Residues in contact with ILE 238 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ASN 4.3 7.2 - - - +
560A GLN* 4.6 11.0 - - - +
563A THR* 5.6 4.9 - - + +
234O ILE 4.2 5.6 - - - +
235O GLU* 3.4 16.2 - - - +
236O LYS 3.2 0.8 - - - -
237O ILE* 1.3 77.9 - - - +
239O SER* 1.3 53.1 + - - +
241O ASP* 3.0 5.2 + - - -
242O VAL* 2.5 54.7 + - + +
371O HIS* 3.5 38.8 - - + +
375O THR* 4.5 16.8 - - + +
378O THR* 3.7 14.4 - - + -
381O ILE* 3.6 20.0 - - + -
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Residues in contact with SER 239 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLN* 5.1 7.6 - - - +
198O PHE* 5.9 3.2 - - - -
200O ASN* 5.1 6.9 + - - -
201O LYS* 5.8 0.2 + - - -
235O GLU 4.0 2.7 + - - -
236O LYS* 3.9 26.6 + - - -
237O ILE 3.4 1.0 - - - -
238O ILE* 1.3 79.2 - - - +
240O ILE* 1.3 67.6 + - - +
242O VAL* 3.9 7.0 + - - +
243O GLU* 3.6 23.4 + - - +
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Residues in contact with ILE 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198O PHE* 6.6 0.2 - - + -
200O ASN* 5.9 0.9 - - - +
201O LYS* 3.6 39.9 - - + +
236O LYS 4.3 10.7 + - - +
237O ILE 3.9 5.0 + - - +
238O ILE 3.4 0.2 - - - -
239O SER* 1.3 82.5 - - - +
241O ASP* 1.3 60.9 + - - +
243O GLU* 3.5 5.1 + - - -
244O LEU* 3.3 25.9 + - + +
328O LEU* 3.5 33.7 - - + +
331O LYS* 6.0 6.1 - - + -
332O LEU* 5.3 13.2 - - + +
335O ILE* 5.1 15.7 - - + -
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Residues in contact with ASP 241 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237O ILE 3.3 18.4 + - - +
238O ILE* 3.0 5.8 + - - +
240O ILE* 1.3 76.1 - - - +
242O VAL* 1.3 64.2 + - - +
244O LEU* 3.1 19.7 + - - +
245O GLN* 3.4 13.5 + - - +
378O THR* 3.1 17.9 - - + +
379O ARG 3.0 30.5 + - - +
380O SER* 2.5 38.3 + - - -
381O ILE* 3.7 7.8 + - - +
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Residues in contact with VAL 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A ALA* 3.3 39.7 - - + +
559A ASN* 3.4 39.2 - - + +
560A GLN* 4.1 12.8 - - + +
238O ILE* 2.5 34.9 + - + +
239O SER* 4.1 7.9 - - - +
240O ILE 3.4 0.2 - - - -
241O ASP* 1.3 72.5 - - - +
243O GLU* 1.3 58.0 + - + +
244O LEU 3.2 1.2 + - - -
245O GLN* 5.5 0.5 - - - +
246O ASN* 2.9 28.8 + - - +
377O TYR 5.8 0.4 - - - -
378O THR* 4.1 4.9 - - + -
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Residues in contact with GLU 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A GLU* 2.9 33.4 - - - +
553A GLN* 5.1 7.9 + - - +
556A ALA* 3.3 25.4 - - - +
201O LYS* 5.3 9.2 - - - +
239O SER 3.6 13.8 + - - +
240O ILE* 3.5 11.1 + - - +
241O ASP 3.3 0.8 - - - -
242O VAL* 1.3 76.6 - - + +
244O LEU* 1.3 54.9 + - - +
246O ASN* 3.4 9.6 - - - -
247O GLU* 3.0 30.1 - - - +
328O LEU* 3.4 10.3 - - + +
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Residues in contact with LEU 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240O ILE* 3.3 20.4 - - + +
241O ASP* 3.1 11.7 + - - +
242O VAL 3.1 1.4 + - - -
243O GLU* 1.3 76.5 - - - +
245O GLN* 1.3 91.9 + - - +
246O ASN 3.3 1.3 - - - -
247O GLU* 3.0 27.6 + - - +
248O LEU* 3.2 8.5 + - + +
328O LEU* 3.8 23.6 - - + +
332O LEU* 4.1 22.9 - - + -
380O SER* 3.9 21.1 - - - +
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Residues in contact with GLN 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241O ASP* 3.4 10.0 + - - +
242O VAL 4.3 0.6 + - - +
244O LEU* 1.3 91.3 - - - +
246O ASN* 1.3 57.4 + - - +
247O GLU 3.2 2.2 - - - -
248O LEU* 3.3 45.4 + - - +
377O TYR* 2.6 52.4 + - + +
378O THR* 4.4 2.0 - - - +
379O ARG* 2.9 58.3 + - + +
591O TYR* 5.8 1.6 - - - -
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Residues in contact with ASN 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A GLU* 3.3 28.6 + - - +
555A LYS* 3.4 62.8 + - + +
556A ALA* 3.4 6.7 - - - +
559A ASN* 5.2 2.0 + - - +
242O VAL 2.9 26.0 + - - +
243O GLU* 3.4 8.0 - - - +
245O GLN* 1.3 77.7 - - - +
247O GLU* 1.3 61.1 + - - +
248O LEU 3.4 1.9 + - - -
377O TYR* 4.1 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
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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