Contacts of the strand formed by residues 199 - 206 (chain O) in PDB entry 2GTL
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 ARG 199 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72M ASP* 2.7 49.1 + - - -
74M PRO* 5.4 1.4 - - - +
108O PHE* 4.7 0.4 - - - -
192O PHE* 4.1 9.7 - - - -
193O ASP* 4.8 5.9 + - - +
196O ASN* 3.4 26.9 + - - +
197O PHE 3.6 0.8 - - - -
198O ASP* 1.3 84.2 - - + +
200O PHE* 1.3 67.7 + - - +
201O VAL* 4.5 13.3 - - - +
217O ILE* 3.5 27.9 - - + +
218O PHE 2.9 14.1 - - - +
219O HIS* 3.9 15.5 - - + +
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Residues in contact with PHE 200 (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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102O THR* 5.0 2.2 - - + -
108O PHE* 3.8 25.6 - + - -
127O LEU* 4.1 16.2 - - + -
176O LEU* 4.3 10.1 - - + -
188O LEU* 5.0 2.9 - - + -
190O GLY* 3.7 22.2 - - - -
191O GLU 4.0 13.0 - - - +
192O PHE* 3.5 43.3 - + + +
193O ASP 5.6 0.2 - - - +
199O ARG* 1.3 78.5 - - - +
201O VAL* 1.3 71.4 + - - +
202O GLY* 4.0 3.4 - - - -
217O ILE* 4.9 0.9 - - - -
218O PHE* 2.9 77.4 + + + -
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Residues in contact with VAL 201 (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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189O VAL 3.9 0.7 - - - +
190O GLY* 3.3 19.1 - - - -
191O GLU* 3.6 17.2 + - + +
199O ARG* 4.5 14.6 - - - +
200O PHE* 1.3 72.4 - - - +
202O GLY* 1.3 61.5 + - - +
203O HIS* 3.8 16.1 + - + +
215O GLU* 4.9 13.9 - - + +
216O PHE 3.7 5.4 - - - +
217O ILE* 4.0 22.2 - - + +
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Residues in contact with GLY 202 (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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188O LEU* 3.7 18.2 - - - +
189O VAL 4.1 1.3 - - - -
200O PHE* 3.5 7.3 + - - -
201O VAL* 1.3 72.1 - - - +
203O HIS* 1.3 63.9 + - - -
204O ILE* 3.9 0.5 + - - +
214O ALA 3.4 1.7 - - - +
215O GLU* 3.4 2.8 - - - -
216O PHE* 2.6 46.4 + - - +
218O PHE* 3.8 11.1 - - - -
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Residues in contact with HIS 203 (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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114O PHE* 5.6 0.2 - + - -
188O LEU* 3.1 3.0 - - - +
189O VAL* 2.8 49.4 + - + +
201O VAL* 3.8 15.4 + - + +
202O GLY* 1.3 75.2 - - - -
204O ILE* 1.3 60.7 + - - +
205O VAL* 3.7 9.6 + - + -
212O VAL* 3.7 35.5 - - + +
214O ALA 3.2 1.3 - - - -
215O GLU* 3.0 43.9 + - + +
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Residues in contact with ILE 204 (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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117O CYS* 4.3 4.7 - - - -
118O THR* 3.6 12.8 - - + +
125O MET* 3.5 34.3 - - + -
186O LEU* 4.2 27.4 - - + -
187O GLY 3.3 12.1 - - - +
188O LEU* 4.4 12.1 - - + -
202O GLY 4.7 0.4 - - - +
203O HIS* 1.3 75.5 - - - +
205O VAL* 1.3 61.2 + - - +
213O CYS* 3.0 29.0 + - - -
214O ALA* 2.6 37.8 + - + +
216O PHE* 3.7 11.4 - - + -
218O PHE* 6.3 0.2 - - + -
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Residues in contact with VAL 205 (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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186O LEU* 3.3 8.0 - - - -
187O GLY 2.7 49.2 + - - +
189O VAL* 4.1 19.3 - - + -
203O HIS* 4.1 13.5 - - + +
204O ILE* 1.3 79.3 - - - +
206O HIS* 1.3 64.5 + - - +
207O GLU* 4.1 18.2 - - - +
210O GLU* 4.1 17.3 - - + +
211O GLU 2.9 22.2 - - - +
212O VAL* 3.7 18.6 - - + +
213O CYS* 4.6 0.2 - - - -
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Residues in contact with HIS 206 (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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10I GLU* 4.5 23.1 - - + +
13I ARG* 5.8 6.9 + - - -
14I GLU* 3.9 35.7 - - + +
117O CYS* 5.0 4.2 - - + +
184O ASP 5.3 2.9 - - - -
185O GLY 3.0 13.0 - - - +
186O LEU* 4.3 12.1 - - + +
205O VAL* 1.3 73.9 - - - +
207O GLU* 1.3 60.3 + - - +
208O LEU* 3.2 1.1 + - + -
209O SER* 4.1 10.5 - - - +
210O GLU* 2.5 33.8 + - - +
211O GLU* 3.2 25.1 + - + +
213O CYS* 3.7 29.1 - - + -
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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