Contacts of the helix formed by residues 198 - 215 (chain B) in PDB entry 2O5C
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 VAL 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 1.3 112.9 - - - +
199B GLN* 1.3 63.5 + - - +
200B THR 3.3 1.8 - - - -
201B PRO* 3.2 11.7 - - - +
202B VAL* 3.2 19.2 + - - +
500B MET* 4.1 12.8 - - + -
522B LEU* 4.0 21.4 - - + +
523B GLY* 4.2 18.2 - - - +
531B ILE* 4.0 25.1 - - + -
4D A 2.9 23.4 + - - +
5D A 5.7 0.2 - - - +
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B SER* 2.8 35.7 + - - +
195B VAL 4.3 0.2 - - - -
196B GLY 3.6 18.6 - - - +
198B VAL* 1.3 73.6 - - - +
200B THR* 1.3 61.3 + - - +
202B VAL 3.5 0.5 + - - -
203B LEU* 3.1 23.7 + - - +
531B ILE* 3.5 20.1 - - + +
534B LEU* 3.3 19.0 - - + +
535B LEU* 3.6 26.7 - - + +
540B PHE* 4.8 0.2 - - - -
3D C 3.2 29.1 + - - -
4D A 2.8 36.7 + - - +
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 5.7 0.2 - - - -
194B SER 4.3 2.2 + - - +
195B VAL* 3.2 19.0 - - + -
196B GLY 2.8 33.6 + - - -
199B GLN* 1.3 77.5 + - - +
201B PRO* 1.4 57.3 - - - +
203B LEU* 3.1 13.7 + - + +
204B GLY* 2.7 31.2 + - - -
535B LEU* 5.6 0.4 - - - -
557B LEU* 5.8 1.3 - - + -
561B LEU* 3.6 30.5 - - + -
565B ALA 3.6 16.2 - - - +
566B THR* 4.1 6.9 - - + +
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY 3.6 2.7 - - - +
197B ARG* 3.3 22.9 - - - +
198B VAL* 3.2 12.1 - - - +
200B THR* 1.4 90.5 - - - +
202B VAL* 1.3 59.4 + - - +
204B GLY* 3.2 0.5 + - - -
205B LEU* 2.9 32.9 + - - +
208B ARG* 4.7 0.9 + - - -
522B LEU* 4.3 11.0 - - + -
565B ALA 3.8 12.6 - - - +
566B THR 3.6 12.8 - - - +
567B ARG 3.9 12.1 - - - +
568B PRO* 4.3 8.0 - - + +
570B MET* 6.5 0.4 - - + -
571B THR* 3.5 20.4 - - + -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B VAL 3.2 17.4 + - - +
199B GLN* 3.6 7.9 - - - +
200B THR 3.3 0.6 - - - -
201B PRO* 1.3 76.0 - - - +
203B LEU* 1.3 62.9 + - - +
205B LEU* 3.4 17.3 + - - +
206B VAL* 3.5 14.4 + - - +
496B LEU* 4.1 28.4 - - + +
500B MET* 3.8 25.4 - - + -
522B LEU* 3.6 19.7 - - + -
531B ILE* 4.2 4.3 - - + -
532B ILE* 4.2 11.9 - - + -
535B LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLN 3.1 14.9 + - - +
200B THR* 3.1 16.6 + - + +
202B VAL* 1.3 75.3 - - - +
204B GLY* 1.3 63.3 + - - +
206B VAL* 3.3 4.5 + - - +
207B VAL* 3.1 30.9 + - + +
535B LEU* 4.1 11.2 - - + +
540B PHE* 3.7 40.8 - - + +
541B LEU* 3.8 20.2 - - + -
550B SER* 4.7 0.2 - - - -
554B GLY* 3.5 29.8 - - - +
557B LEU* 4.4 14.8 - - + -
558B PHE* 4.7 7.6 - - + +
566B THR* 6.3 0.4 - - + -
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR 2.7 15.3 + - - -
201B PRO 3.2 4.9 + - - -
203B LEU* 1.3 73.6 - - - +
205B LEU* 1.3 59.8 + - - +
208B ARG* 3.1 37.7 + - - +
558B PHE* 3.7 20.7 - - - -
566B THR* 3.5 15.9 - - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO 2.9 19.5 + - - +
202B VAL* 3.5 13.7 - - - +
203B LEU 3.3 0.4 - - - -
204B GLY* 1.3 75.6 - - - +
206B VAL* 1.3 60.3 + - - +
208B ARG* 3.8 18.7 - - - +
209B ARG* 3.1 23.9 + - - +
491B PHE* 3.5 9.5 - - + -
496B LEU* 4.1 17.0 - - + -
499B ALA* 3.8 24.2 - - + -
500B MET* 4.7 6.1 - - + +
503B ILE* 4.3 20.0 - - + -
506B PHE* 3.8 42.0 - - + -
522B LEU* 4.9 0.4 - - + -
568B PRO* 5.3 2.7 - - + -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL 3.5 13.4 + - - +
203B LEU 3.3 7.2 + - - +
205B LEU* 1.3 71.5 - - - +
207B VAL* 1.3 58.1 + - - +
209B ARG* 3.2 2.3 + - - +
210B ASP* 2.8 46.2 + - - +
491B PHE* 4.1 14.8 - - + -
496B LEU* 3.8 31.4 - - + -
541B LEU* 3.9 22.2 - - + -
548B ILE* 4.3 12.3 - - + +
549B HIS 4.1 2.9 - - - -
550B SER* 3.6 28.3 - - - +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.1 25.1 + - + +
204B GLY 4.1 0.2 - - - +
206B VAL* 1.3 73.0 - - - +
208B ARG* 1.3 58.6 + - - +
210B ASP* 3.2 1.6 + - - +
211B GLU* 2.9 49.2 + - - +
550B SER* 3.7 27.8 - - - -
554B GLY 4.1 4.3 - - - +
555B LYS* 4.1 17.7 - - + -
558B PHE* 3.5 51.4 - - + -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO 4.7 0.6 + - - -
204B GLY* 3.1 21.9 + - - +
205B LEU* 3.8 33.6 - - - +
207B VAL* 1.3 76.9 - - - +
209B ARG* 1.3 56.6 + - - +
211B GLU* 3.4 5.6 + - - +
212B GLU* 3.0 31.9 + - - +
506B PHE* 5.5 2.4 + - - +
558B PHE* 3.8 22.4 - - + -
566B THR* 3.0 30.9 + - - -
567B ARG* 3.7 45.8 - - - +
568B PRO* 3.8 20.6 - - - +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU 3.1 19.0 + - - +
206B VAL 3.5 3.8 - - - +
208B ARG* 1.3 76.3 - - - +
210B ASP* 1.3 64.7 + - - +
212B GLU* 3.2 16.2 + - - +
213B ILE* 3.1 29.0 + - + +
488B PRO* 3.8 24.6 - - - +
489B ARG* 2.7 43.4 + - - +
490B HIS* 4.4 7.9 + - - -
491B PHE* 3.4 49.4 - - + +
495B THR* 5.7 1.2 + - - -
506B PHE* 4.3 16.2 - - - -
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 2.8 27.6 + - - +
207B VAL 3.7 3.8 - - - +
209B ARG* 1.3 77.3 - - - +
211B GLU* 1.3 58.1 + - - +
213B ILE* 3.5 3.3 + - - +
214B GLU* 3.0 29.7 + - - +
490B HIS* 3.0 36.1 + - + +
491B PHE 5.3 0.7 + - - -
548B ILE 4.1 2.9 - - - +
549B HIS* 3.6 3.7 - - - +
550B SER* 2.6 45.3 + - - +
555B LYS* 4.0 12.5 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 2.9 30.8 + - + +
208B ARG* 4.2 4.8 - - - +
210B ASP* 1.3 74.8 - - - +
212B GLU* 1.3 59.3 + - - +
214B GLU* 3.8 13.2 - - + +
215B ASN* 2.9 47.8 + - - +
555B LYS* 3.9 24.3 - - - +
558B PHE* 4.5 2.6 - - - -
559B HIS* 2.7 42.0 + - - -
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG 3.0 17.0 + - - +
209B ARG* 3.2 20.6 + - - +
211B GLU* 1.3 78.2 - - - +
213B ILE* 1.3 56.1 + - - +
215B ASN* 3.5 3.4 + - - +
216B PHE* 3.0 30.7 + - + +
488B PRO* 3.9 25.3 - - + +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ARG* 3.1 18.8 + - + +
210B ASP* 3.7 5.8 - - - +
212B GLU* 1.3 74.6 - - - +
214B GLU* 1.3 66.7 + - - +
216B PHE* 3.2 21.3 + - - +
487B PRO* 4.7 11.6 - - + +
488B PRO* 3.4 37.0 - - + +
489B ARG 3.7 4.9 - - - +
490B HIS* 3.6 56.5 - - + +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP* 3.0 20.4 + - - +
211B GLU* 3.5 15.9 - - - +
213B ILE* 1.3 79.2 - - - +
215B ASN* 1.3 66.9 + - - +
216B PHE 3.5 2.3 - - - +
555B LYS* 4.0 22.1 + - - +
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Residues in contact with ASN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLU* 2.9 33.3 + - - +
212B GLU* 3.8 3.6 - - - +
214B GLU* 1.3 84.6 - - - +
216B PHE* 1.3 66.3 + - - +
217B VAL* 3.5 12.3 + - - +
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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
------------------------------------------------------------
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