Contacts of the strand formed by residues 190 - 196 (chain O) in PDB entry 6GYK
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 PHE 190 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22N T 4.5 5.8 - - - +
23N A 3.2 59.0 - + - +
184O SER 5.5 0.2 - - - -
185O TYR* 4.5 0.2 - - - -
186O GLU* 2.6 29.8 + - + +
187O PRO* 3.7 1.9 + - - +
189O LEU* 1.3 76.0 - - + +
191O PRO* 1.3 78.1 - - + +
192O GLY* 3.0 52.3 + - - +
193O LEU 4.0 1.1 - - - -
194O ILE* 3.9 26.0 - - + -
205O LEU* 4.1 13.9 - - + -
207O PHE* 3.6 28.3 - + - -
64T A 5.4 4.7 - + - -
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Residues in contact with PRO 191 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272M LYS* 5.0 9.9 - - - +
273M SER 5.4 0.2 - - - +
22N T 4.7 7.0 - - - +
172O LEU* 3.5 9.5 - - - +
185O TYR* 3.3 19.8 + - - -
187O PRO* 3.8 19.5 - - + +
189O LEU 4.7 0.7 - - - -
190O PHE* 1.3 93.4 - - + +
192O GLY* 1.3 56.1 + - - +
207O PHE* 4.8 4.6 - - + -
208O VAL* 4.6 8.1 - - + +
64T A 4.6 13.2 - - + +
65T T 3.9 41.1 - - - +
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Residues in contact with GLY 192 (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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184O SER 4.5 0.5 - - - +
185O TYR* 3.5 12.8 - - - -
186O GLU 4.6 0.2 + - - -
190O PHE* 3.0 49.5 + - - +
191O PRO* 1.3 79.5 - - - +
193O LEU* 1.3 58.2 + - - -
194O ILE 4.3 0.5 + - - -
206O ILE 3.7 9.6 - - - -
207O PHE* 3.9 13.1 - - - -
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Residues in contact with LEU 193 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172O LEU* 3.5 35.0 - - + +
175O LEU* 3.9 29.8 - - + -
176O ALA* 4.0 7.4 - - + +
183O SER* 3.4 26.9 - - - +
184O SER 4.4 1.3 - - - +
185O TYR* 4.0 20.4 - - + -
190O PHE* 4.0 0.9 - - - -
192O GLY* 1.3 74.2 - - - -
194O ILE* 1.3 63.9 + - - +
195O TYR* 3.7 19.2 + - + +
204O LEU 3.2 1.6 - - - +
205O LEU* 3.2 8.5 - - - -
206O ILE* 2.9 44.2 + - + +
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Residues in contact with ILE 194 (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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23N A 2.9 34.1 - - - +
24N T 3.0 33.4 - - - +
182O PHE 3.4 2.8 - - - +
183O SER* 3.3 3.6 - - - -
184O SER* 3.1 48.0 + - - +
190O PHE* 3.9 22.2 - - + -
193O LEU* 1.3 78.0 - - - +
195O TYR* 1.3 57.5 + - - +
196O ARG* 3.8 18.0 + - + +
203O VAL* 4.1 19.7 - - + -
204O LEU 3.6 2.2 - - - -
205O LEU* 4.1 6.5 - - + -
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Residues in contact with TYR 195 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175O LEU* 5.0 6.3 - - + -
179O HIS* 4.0 31.1 + + + -
182O PHE* 3.3 32.3 - + + -
183O SER* 3.3 18.4 - - - -
193O LEU* 3.7 14.3 + - + -
194O ILE* 1.3 72.4 - - - +
196O ARG* 1.3 59.1 + - - +
197O MET* 3.8 34.3 - - + +
202O ILE 3.6 3.1 - - - +
203O VAL* 3.6 1.2 - - - +
204O LEU* 2.9 48.7 + - + +
206O ILE* 4.2 10.8 - - + -
230O ILE* 3.7 31.7 - - + +
233O VAL* 5.6 3.0 - - + +
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Residues in contact with ARG 196 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208M ASN* 5.3 6.9 - - - +
24N T 3.9 25.0 + - - -
25N A 4.1 21.2 + - - -
182O PHE* 2.7 43.9 + - - +
184O SER* 5.9 4.6 - - - -
194O ILE* 4.6 18.2 - - + +
195O TYR* 1.3 74.1 - - - +
197O MET* 1.3 64.5 + - - +
198O VAL* 3.8 0.9 + - - +
201O LYS* 5.9 2.2 - - - +
202O ILE 3.9 3.8 - - - -
203O VAL* 4.3 23.2 - - + +
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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