Contacts of the strand formed by residues 219 - 226 (chain G) in PDB entry 6G2T
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 219 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158G VAL* 4.7 12.6 - - + -
177G ARG* 3.5 49.8 - - + +
178G VAL 3.6 9.0 - - - +
179G ALA* 4.8 7.9 - - + -
213G TYR* 4.7 1.8 - - - -
214G ASP* 3.7 26.1 + - - +
217G SER* 3.0 33.0 + - - +
218G LYS* 1.3 78.9 - - - +
220G TYR* 1.3 66.7 - - - +
221G LEU* 3.8 2.9 + - + +
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Residues in contact with TYR 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G ALA 3.6 1.2 - - - +
177G ARG* 3.3 5.4 - - - -
178G VAL* 2.8 46.5 + - + +
180G GLY* 3.9 23.8 - - - -
185G LYS 5.0 1.2 - - - -
186G PRO* 3.7 32.3 - - + +
187G PRO* 3.7 24.5 - - + -
212G SER 3.9 4.7 - - - -
213G TYR* 3.2 51.5 + + + -
219G VAL* 1.3 75.6 - - - +
221G LEU* 1.3 60.7 + - - +
222G PHE* 3.9 25.5 + + + -
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Residues in contact with LEU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G MET* 6.3 0.4 - - - -
175G SER* 3.8 27.8 - - - +
176G ALA 3.8 2.9 - - - +
177G ARG* 3.7 38.6 - - + +
210G HIS* 4.1 0.3 - - - +
211G ASP* 3.9 1.0 - - - -
212G SER* 3.1 48.3 + - - +
219G VAL* 3.8 3.4 + - + +
220G TYR* 1.3 72.1 - - - +
222G PHE* 1.3 64.0 + - - +
223G GLU* 3.5 28.9 + - + +
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Residues in contact with PHE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G SER* 3.1 4.9 - - - -
176G ALA* 2.9 40.0 + - + +
178G VAL* 3.8 30.7 - - + -
187G PRO* 3.4 39.0 - - + -
189G VAL* 3.5 39.3 - - + -
191G TRP* 4.0 8.3 - - + +
211G ASP* 3.2 34.8 - - + +
212G SER 5.1 1.8 - - - -
220G TYR* 3.9 21.3 - + + -
221G LEU* 1.3 79.4 - - - +
223G GLU* 1.3 61.5 + - - +
241G VAL* 4.1 6.1 - - + -
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Residues in contact with GLU 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G THR* 4.5 8.8 - - + +
174G PHE 3.5 3.1 - - - +
175G SER* 3.7 18.1 - - - -
191G TRP* 4.4 4.7 + - - +
209G LEU* 3.7 8.7 - - - +
210G HIS* 2.8 55.4 + - + +
211G ASP* 4.3 1.3 + - - +
212G SER* 5.8 0.9 - - - -
221G LEU* 3.5 25.8 - - + +
222G PHE* 1.3 78.1 - - - +
224G LEU* 1.3 59.9 + - - +
225G HIS* 3.0 33.5 + - + +
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Residues in contact with LEU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G ILE 4.0 1.0 - - - +
173G THR* 3.5 5.4 - - - +
174G PHE* 2.7 46.1 + - + +
191G TRP* 3.6 35.2 - - + -
199G LEU* 3.7 21.8 - - + -
207G LEU* 4.0 23.3 - - + -
208G GLN 4.0 2.2 - - - +
209G LEU* 3.5 23.8 - - + -
223G GLU* 1.3 72.3 - - - +
225G HIS* 1.3 64.3 + - - +
226G ILE* 4.0 21.4 + - + +
237G TYR* 4.5 1.6 - - + -
252G PHE* 4.1 12.3 - - + -
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Residues in contact with HIS 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G ILE 4.1 1.3 - - - -
173G THR* 3.1 32.1 + - + -
206G HIS 4.0 0.3 - - - +
207G LEU* 3.5 5.0 - - - +
208G GLN* 2.8 59.5 + - + +
209G LEU 4.8 0.2 - - - -
210G HIS* 3.8 24.0 - - + +
223G GLU* 3.0 30.6 + - + +
224G LEU* 1.3 74.8 - - - +
226G ILE* 1.3 64.6 - - - +
227G THR* 5.1 8.2 - - + +
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Residues in contact with ILE 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G GLY 4.1 0.3 - - - +
171G SER* 3.3 2.9 - - - -
172G ILE* 2.8 53.4 + - + +
174G PHE* 4.5 6.5 - - + -
206G HIS 3.7 4.0 - - - +
207G LEU* 4.7 12.8 - - + -
224G LEU* 4.3 20.2 - - + +
225G HIS* 1.3 78.1 - - - +
227G THR* 1.3 63.9 + - - +
229G ALA* 4.3 12.6 - - + -
233G PHE* 4.0 31.0 - - + -
237G TYR* 3.8 17.0 - - + +
254G LEU* 3.5 28.9 - - + -
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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