Contacts of the strand formed by residues 197 - 202 (chain A) in PDB entry 2GPY
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 TYR 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A PHE* 4.0 13.7 - + + -
147A SER* 3.2 24.5 + - - -
156A ILE* 3.6 22.9 - - + -
191A LEU* 5.2 1.5 - - + +
192A LEU 4.9 4.5 - - - +
194A HIS* 3.1 52.0 + + + +
195A PRO 3.3 1.0 - - - -
196A GLN* 1.3 91.1 + - + +
198A ASP* 1.3 59.8 + - - +
199A THR* 3.7 17.2 + - - +
211A SER* 4.0 18.2 - - - +
212A ILE 3.4 1.3 - - - -
213A LYS* 3.4 59.5 + - + +
214A ARG* 2.8 19.0 + - - -
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TYR* 1.3 72.4 - - - +
199A THR* 1.3 61.3 + - - +
211A SER* 3.5 0.2 - - - -
212A ILE* 2.9 43.3 + - + +
214A ARG* 3.6 29.5 + - + +
48B HIS* 3.2 10.1 - - - -
51B LYS* 2.8 29.8 + - - +
310B ZN 3.0 25.4 - - - -
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 4.1 15.6 + - + +
192A LEU* 4.1 36.3 + - + +
197A TYR* 3.7 12.6 + - - +
198A ASP* 1.3 76.9 + - - +
200A ARG* 1.3 64.9 + - - +
209A ALA* 4.0 19.5 - - + -
210A ILE 3.4 6.1 - - - +
211A SER* 2.7 33.1 + - - +
15B GLN* 4.6 2.4 - - - +
48B HIS* 3.9 2.2 - - - -
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 5.8 0.2 - - - -
199A THR* 1.3 76.2 - - - +
201A ILE* 1.3 69.7 + - - +
202A PHE* 3.8 9.8 - - + -
208A ILE 3.8 0.2 - - - +
209A ALA* 4.4 0.4 - - - -
210A ILE* 2.7 41.8 + - - +
15B GLN* 2.9 59.4 + - - +
17B PRO* 4.9 4.8 - - - +
41B LEU* 3.9 26.1 + - - +
44B GLU* 3.5 41.3 + - - +
45B SER* 3.5 18.8 + - - +
48B HIS* 3.5 32.0 + - + +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 3.8 25.8 - - + -
162A LEU* 4.0 18.8 - - + -
192A LEU* 4.3 20.0 - - + -
200A ARG* 1.3 77.0 + - - +
202A PHE* 1.3 73.2 + - - +
203A PRO* 4.5 1.0 - - - +
207A GLY* 4.1 9.0 - - - -
208A ILE 3.4 15.0 - - - +
209A ALA* 4.2 5.4 - - + -
11B TYR* 3.8 26.2 - - + +
12B LEU* 3.7 24.3 - - + +
15B GLN* 3.0 33.3 + - - +
45B SER* 5.5 0.9 + - - -
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 5.4 4.0 - - + -
200A ARG* 3.8 15.3 - - + -
201A ILE* 1.3 82.7 - - - +
203A PRO* 1.3 72.5 - - + +
204A VAL* 2.8 16.3 + - + -
207A GLY* 3.5 4.2 - - - -
208A ILE* 2.8 39.0 + - + +
210A ILE* 3.3 25.6 - - + -
12B LEU* 4.7 0.9 - - - -
45B SER* 3.6 47.3 - - - -
48B HIS* 3.7 27.4 - + + -
49B LEU* 3.8 27.8 - - + -
202B PHE* 5.5 6.1 - + - -
204B VAL* 5.3 4.9 - - + -
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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