Contacts of the strand formed by residues 197 - 202 (chain A) in PDB entry 6GR2
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 HIS 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A MET* 3.9 6.8 - - - +
56A ALA 4.8 2.1 + - - -
189A ILE* 5.9 0.5 - - - +
194A GLN* 3.1 30.4 + - + +
195A LYS 3.0 22.3 + - - -
196A GLY* 1.3 80.9 + - - +
198A ALA* 1.3 65.7 + - - +
210A LEU* 3.9 27.9 - - + +
211A VAL 3.3 7.9 - - - +
212A PRO* 3.5 35.1 - - + +
213A LEU* 3.9 2.7 - - - +
383A ALA* 3.1 21.2 - - - +
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Residues in contact with ALA 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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40A LEU* 4.1 21.5 - - + -
53A LEU* 4.0 17.7 - - + -
54A PRO 3.5 11.4 - - - +
55A MET* 4.2 2.7 - - + -
197A HIS* 1.3 75.8 - - - +
199A LEU* 1.3 63.1 + - - +
200A LEU 4.0 0.7 - - - -
209A SER 3.6 0.9 - - - +
210A LEU* 3.6 3.5 - - - -
211A VAL* 2.8 37.9 + - + +
213A LEU* 4.1 12.5 - - + +
295A LEU* 4.7 4.7 - - + -
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Residues in contact with LEU 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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52A VAL 3.3 1.2 - - - +
53A LEU* 3.5 3.0 - - - -
54A PRO* 2.8 46.2 + - - +
188A PHE* 4.7 1.3 - - + -
189A ILE* 3.9 17.2 - - + +
192A MET* 3.3 49.6 - - + +
193A GLY* 5.0 1.1 - - - -
198A ALA* 1.3 71.3 - - - +
200A LEU* 1.3 62.2 - - - +
201A ILE* 3.3 18.8 + - + +
208A THR* 4.3 8.5 - - - +
209A SER 3.1 26.7 - - - +
210A LEU* 3.2 29.6 - - + -
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Residues in contact with LEU 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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51A LEU* 4.6 19.3 - - + -
52A VAL 3.3 14.1 - - - +
53A LEU* 3.7 14.3 - - + +
198A ALA 4.0 0.6 + - - -
199A LEU* 1.3 68.7 - - - +
201A ILE* 1.3 61.6 + - - +
202A ASP 4.0 0.4 + - - +
207A GLU 3.8 0.9 - - - +
208A THR* 3.4 4.5 - - - -
209A SER* 2.9 44.2 + - - +
211A VAL* 4.4 5.1 - - + +
288A THR* 4.2 18.6 - - + +
289A ALA* 5.4 2.2 - - - -
292A ALA* 3.9 21.8 - - + -
296A ARG* 3.4 28.5 - - - +
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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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51A LEU* 3.4 8.7 - - - +
52A VAL* 2.9 49.9 + - + +
54A PRO* 3.9 17.5 - - + -
184A ILE* 4.5 7.6 - - + -
185A MET* 4.6 4.5 - - + +
188A PHE* 3.9 37.2 - - + -
189A ILE* 4.6 4.0 - - + +
199A LEU* 3.7 21.5 - - + +
200A LEU* 1.3 74.3 - - - +
202A ASP* 1.3 70.1 + - - +
203A CYS* 3.5 13.3 + - - -
206A LEU* 5.1 1.8 - - + -
207A GLU 3.7 2.5 - - - -
208A THR* 4.3 19.7 - - + -
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Residues in contact with ASP 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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51A LEU* 3.8 13.4 - - + +
200A LEU* 4.0 1.2 + - - +
201A ILE* 1.3 70.1 - - - +
203A CYS* 1.3 54.1 + - - +
204A ARG* 3.0 12.7 + - - +
205A SER* 3.3 23.8 + - - +
206A LEU* 2.6 38.8 + - - -
207A GLU* 2.9 24.4 + - + +
256A ARG* 2.5 43.5 + - - -
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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