Contacts of the helix formed by residues 200 - 212 (chain B) in PDB entry 6G4O
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 SER 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY* 4.2 0.2 - - - -
199B GLU* 1.3 91.3 - - - +
201B ALA* 1.3 59.0 + - - -
203B GLY 3.1 0.2 + - - -
204B ALA 2.9 22.9 + - - -
225B GLN 2.8 13.5 + - - -
226B SER 3.4 15.5 - - - -
227B GLY* 3.5 9.4 - - - -
233B TRP* 3.7 8.6 - - - -
440B HIS* 3.2 2.5 + - - -
603B ELT 1.6 57.2 + - - -
609B P6G 4.1 0.7 - - - -
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Residues in contact with ALA 201 (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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116B TYR 4.4 1.3 - - - -
117B GLY* 4.0 5.8 - - - -
119B GLY* 3.6 16.2 - - - +
120B PHE* 3.6 32.6 - - + +
148B TYR* 4.7 2.0 - - - +
200B SER* 1.3 81.4 + - - +
202B GLY* 1.3 58.3 + - - +
204B ALA* 3.8 2.7 - - - +
205B SER* 2.9 28.4 + - - -
233B TRP* 4.0 11.2 - - + -
603B ELT 3.0 16.7 + - - +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.3 27.9 - - - +
116B TYR 3.7 7.0 - - - -
117B GLY* 3.5 4.2 - - - -
198B GLY* 3.5 7.9 - - - -
199B GLU 2.6 21.0 + - - -
201B ALA* 1.3 69.0 - - - +
203B GLY* 1.3 61.6 + - - -
205B SER* 3.3 4.0 + - - -
206B VAL* 3.1 25.5 + - - +
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Residues in contact with GLY 203 (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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198B GLY 3.1 22.9 + - - -
199B GLU 3.3 1.2 - - - -
200B SER 3.1 7.9 + - - -
202B GLY* 1.3 73.2 - - - +
204B ALA* 1.3 63.3 + - - +
205B SER 3.3 0.2 + - - -
206B VAL* 3.3 5.9 + - - +
207B GLY 3.1 17.7 + - - -
224B LEU* 3.5 12.6 - - - +
225B GLN 4.2 9.0 - - - -
227B GLY 3.9 14.1 - - - -
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.4 5.4 - - + -
200B SER 2.9 14.6 + - - +
201B ALA* 3.5 6.3 + - - +
202B GLY 3.3 0.2 - - - -
203B GLY* 1.3 77.0 - - - +
205B SER* 1.3 57.2 + - - +
207B GLY* 3.4 1.9 + - - -
208B MET* 2.9 35.1 + - + +
228B SER 3.5 31.2 - - - +
229B PRO* 3.8 3.5 - - + +
233B TRP* 4.1 14.1 - - + -
234B ALA* 4.2 13.5 - - + -
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 4.4 4.9 - - - -
120B PHE* 3.2 19.4 - - - -
148B TYR* 4.9 0.3 + - - -
170B LEU* 3.9 3.2 - - - +
173B GLN* 3.4 33.1 + - - -
201B ALA 2.9 21.6 + - - -
202B GLY* 3.6 6.4 - - - -
203B GLY 3.2 0.2 - - - -
204B ALA* 1.3 74.6 - - - +
206B VAL* 1.3 55.6 + - - +
208B MET* 2.9 12.2 + - - +
209B HIS* 2.8 42.0 + - - -
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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
----------------------------------------------------------
115B ILE* 3.8 11.1 - - + +
196B ILE* 4.0 13.4 - - + +
197B PHE* 3.5 27.6 - - - +
198B GLY 3.8 0.4 - - - +
202B GLY 3.1 16.3 + - - +
203B GLY 3.4 8.3 - - - +
205B SER* 1.3 74.6 - - - +
207B GLY* 1.3 63.7 + - - +
209B HIS* 3.2 6.5 + - - +
210B ILE* 3.0 21.5 + - + +
222B ALA* 3.8 21.5 - - + -
223B ILE 3.3 29.4 - - - +
224B LEU* 3.4 15.7 - - + -
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLY 3.1 11.1 + - - -
204B ALA 3.6 3.8 - - - -
206B VAL* 1.3 76.5 - - - +
208B MET* 1.3 61.0 + - - +
210B ILE* 3.2 10.8 + - - +
211B LEU* 3.2 25.6 + - - +
224B LEU* 3.6 18.1 - - - +
229B PRO* 3.7 18.4 - - - +
407B PHE* 4.6 2.6 - - - -
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Residues in contact with MET 208 (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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120B PHE* 4.4 4.3 - - + -
170B LEU* 3.9 12.6 - - + -
204B ALA* 2.9 27.0 + - + +
205B SER* 2.9 8.6 + - - +
207B GLY* 1.3 76.8 - - - +
209B HIS* 1.3 59.0 + - + +
211B LEU* 3.2 3.3 + - - +
212B SER* 2.8 29.5 + - - -
229B PRO* 3.8 27.8 - - + +
234B ALA* 3.4 33.9 - - + +
235B SER* 4.8 4.7 - - - -
294B PRO* 3.7 23.8 - - + -
300B PHE* 3.9 8.4 - - + -
301B PHE* 3.4 36.3 - - + -
305B LEU* 5.0 1.6 - - + -
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Residues in contact with HIS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 5.3 5.6 - - + -
170B LEU* 3.9 20.1 - - + +
173B GLN* 3.0 29.3 + - - +
174B ARG* 4.2 12.8 - - + -
177B LEU* 4.4 14.4 - - + +
196B ILE* 4.0 10.1 - - + -
205B SER* 2.8 27.8 + - - -
206B VAL* 3.2 6.0 + - - +
208B MET* 1.3 73.9 - - - +
210B ILE* 1.3 63.7 + - - +
211B LEU 3.1 1.3 + - - -
212B SER 3.6 13.5 + - - +
215B SER* 2.7 39.3 + - - -
216B ARG* 3.9 3.6 - - - +
219B PHE* 3.7 23.0 - - + -
300B PHE* 3.9 14.3 - + - -
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Residues in contact with ILE 210 (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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206B VAL 3.0 16.6 + - - +
207B GLY* 3.2 9.6 + - - +
209B HIS* 1.3 77.0 - - - +
211B LEU* 1.3 66.1 + - + +
216B ARG* 3.5 5.0 + - - +
219B PHE* 4.0 18.6 - - + -
222B ALA* 3.6 14.8 - - + -
224B LEU* 4.6 4.0 - - + -
314B PHE* 3.4 11.6 - - + +
315B LYS* 3.0 52.1 + - + +
319B ILE* 3.5 31.9 - - + -
407B PHE* 4.4 15.0 - - + -
411B TYR* 3.9 13.2 - - + +
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Residues in contact with LEU 211 (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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207B GLY 3.2 15.7 + - - +
208B MET 3.2 5.6 + - - +
209B HIS 3.1 0.2 - - - -
210B ILE* 1.3 83.5 - - + +
212B SER* 1.3 62.2 + - - +
213B PRO* 3.1 4.7 - - - +
216B ARG* 3.1 19.9 + - - -
229B PRO* 4.5 13.0 - - + -
301B PHE* 4.5 7.6 - - + -
305B LEU* 3.9 44.0 - - + +
308B MET* 3.2 22.2 - - + +
309B LEU* 4.0 23.6 - - + -
313B ASN 4.6 1.8 - - - +
314B PHE* 3.6 27.1 - - + -
407B PHE* 4.7 4.9 - - + -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 3.7 12.6 + - - -
208B MET 2.8 17.9 + - - -
209B HIS 3.6 0.9 + - - +
210B ILE 3.6 0.6 - - - -
211B LEU* 1.3 75.2 - - - +
213B PRO* 1.3 68.9 - - - +
214B GLY 4.0 2.3 + - - -
215B SER* 3.1 21.6 + - - -
216B ARG* 3.1 16.6 + - - +
300B PHE* 2.7 46.6 + - - -
301B PHE* 5.3 0.7 - - - -
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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