Contacts of the strand formed by residues 202 - 209 (chain t) in PDB entry 5GJQ
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 GLY 202 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48t ASP* 4.0 16.2 - - - -
197t ILE 3.5 2.8 - - - +
198t VAL* 3.6 1.9 - - - -
199t THR* 3.0 36.6 + - - +
200t LYS 3.2 0.8 - - - -
201t GLU* 1.3 82.8 - - - +
203t ILE* 1.3 64.1 + - - -
204t ARG 4.1 0.8 + - - -
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Residues in contact with ILE 203 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45t LYS* 4.2 17.5 - - + -
47t THR 3.6 23.8 - - - +
48t ASP* 3.9 17.7 - - - +
50t THR 4.5 0.7 - - - +
51t VAL* 3.8 28.0 - - + -
196t CYS* 4.3 12.3 - - + -
197t ILE 3.2 9.0 - - - +
198t VAL* 4.2 11.2 - - + -
202t GLY* 1.3 76.4 - - - +
204t ARG* 1.3 70.6 + - - +
205t GLU* 4.1 5.9 + - + +
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Residues in contact with ARG 204 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168t LEU* 6.0 3.8 - - - +
195t ILE 3.7 0.2 - - - +
196t CYS* 3.3 5.5 - - - -
197t ILE* 2.9 54.5 + - + +
202t GLY 4.1 0.6 + - - -
203t ILE* 1.3 76.5 - - - +
205t GLU* 1.3 67.5 + - - +
206t GLU* 3.7 27.9 + - - +
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Residues in contact with GLU 205 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43t CYS* 5.5 1.6 - - - +
194t ARG* 4.0 35.4 + - + +
195t ILE 3.3 4.0 - - - +
196t CYS* 4.0 24.8 - - - -
197t ILE* 4.8 0.4 - - - -
203t ILE* 4.1 6.0 + - + +
204t ARG* 1.3 89.1 + - - +
206t GLU* 1.3 60.2 + - - +
207t THR* 4.5 2.4 + - - +
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Residues in contact with GLU 206 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172t MET* 3.3 29.5 - - + +
176t LYS* 2.4 34.7 + - - +
193t LEU 3.8 0.7 - - - +
194t ARG* 3.4 1.2 - - - +
195t ILE* 2.8 38.9 + - + +
197t ILE* 4.5 4.5 - - + +
204t ARG* 3.7 20.9 + - - +
205t GLU* 1.3 74.5 - - - +
207t THR* 1.3 69.3 + - - +
208t VAL* 4.3 8.5 - - + +
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Residues in contact with THR 207 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27t THR* 5.7 2.0 - - + -
192t ALA* 4.6 9.9 - - + -
193t LEU 3.3 15.5 - - - +
194t ARG* 3.4 34.5 + - - +
205t GLU* 5.2 2.6 - - - +
206t GLU* 1.3 79.8 + - - +
208t VAL* 1.3 72.8 + - - +
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Residues in contact with VAL 208 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176t LYS* 3.8 46.7 - - + +
180t ILE* 5.9 6.5 - - + -
192t ALA* 3.5 4.6 - - - +
193t LEU* 2.9 45.4 + - + +
195t ILE* 4.3 11.4 - - + -
206t GLU* 4.6 2.9 - - + -
207t THR* 1.3 83.9 - - - +
209t SER* 1.3 73.5 + - - +
210t LEU* 5.4 1.3 - - + -
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Residues in contact with SER 209 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180t ILE* 5.2 3.1 - - - +
191t ASP 4.5 2.9 - - - -
192t ALA* 4.6 1.6 - - - +
208t VAL* 1.3 85.2 - - - +
210t LEU* 1.3 79.1 + - - +
212t LYS* 3.6 13.9 + - - +
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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