Contacts of the strand formed by residues 197 - 202 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C MET* 3.8 6.6 - - - +
56C ALA 4.8 1.6 + - - -
193C GLY* 5.9 0.3 - - - -
194C GLN* 3.1 29.4 + - + +
195C LYS 2.9 22.8 + - - -
196C GLY* 1.3 81.1 + - - +
198C ALA* 1.3 65.0 + - - +
199C LEU* 5.8 0.6 - - + +
210C LEU* 3.9 27.4 - - + +
211C VAL 3.3 8.5 - - - +
212C PRO* 3.6 32.2 - - + +
213C LEU* 3.9 2.9 - - - +
383C ALA* 3.0 21.4 - - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.8 24.7 - - + -
53C LEU* 3.7 19.1 - - + -
54C PRO 3.5 11.7 - - - +
55C MET* 4.1 3.1 - - + -
189C ILE* 5.8 0.2 - - - -
197C HIS* 1.3 75.2 - - - +
199C LEU* 1.3 65.8 + - - +
200C LEU 4.0 0.7 - - - -
209C SER 3.7 1.0 - - - +
210C LEU* 3.8 1.2 - - - -
211C VAL* 2.8 37.8 + - + +
213C LEU* 4.0 10.5 - - + +
295C LEU* 4.5 2.5 - - + -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL 3.1 1.0 - - - +
53C LEU* 3.4 3.4 - - - -
54C PRO* 2.7 45.4 + - - +
55C MET* 4.9 0.2 - - - +
188C PHE* 5.1 0.2 - - + -
189C ILE* 3.9 16.8 - - + -
192C MET* 3.4 43.5 - - + +
193C GLY* 4.8 2.9 - - - -
194C GLN 5.2 0.9 - - - +
197C HIS 5.8 0.9 - - - +
198C ALA* 1.3 70.7 - - - +
200C LEU* 1.3 62.1 + - - +
201C ILE* 3.3 14.9 + - + +
208C THR* 3.0 35.4 - - + -
209C SER 3.3 8.5 - - - +
210C LEU* 3.1 30.1 - - + -
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Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 4.1 22.0 - - + -
52C VAL 3.1 18.8 - - - +
53C LEU* 3.5 13.5 - - + +
199C LEU* 1.3 71.1 - - - +
201C ILE* 1.3 60.1 + - - +
202C ASP 4.0 0.4 + - - +
207C GLU 3.9 0.9 - - - +
208C THR* 3.5 4.0 - - - -
209C SER* 3.0 44.6 + - - +
211C VAL* 4.3 4.5 - - + -
288C THR* 3.6 25.1 - - + +
289C ALA* 5.0 7.2 - - + +
292C ALA* 3.6 17.5 - - + -
296C ARG* 3.6 23.8 - - - +
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLY 3.7 0.2 - - - +
51C LEU* 3.3 7.8 - - - -
52C VAL* 2.8 42.5 + - + +
54C PRO* 3.9 25.1 - - + -
184C ILE* 4.7 4.3 - - + -
185C MET* 4.7 3.4 - - + +
188C PHE* 3.9 48.7 - - + -
189C ILE* 4.4 7.6 - - + +
199C LEU* 3.6 24.0 - - + +
200C LEU* 1.3 73.9 - - - +
202C ASP* 1.3 71.4 + - - +
203C CYS* 3.5 12.7 + - - -
206C LEU* 4.9 2.7 - - + -
207C GLU 3.7 6.7 - - - +
208C THR* 4.7 3.4 - - + +
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Residues in contact with ASP 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.5 13.9 - - + +
200C LEU* 4.0 1.2 + - - +
201C ILE* 1.3 70.1 - - - +
203C CYS* 1.3 54.6 + - - +
204C ARG* 2.9 24.8 + - - +
205C SER* 3.2 19.8 + - - +
206C LEU* 2.5 40.1 + - - -
207C GLU* 3.0 19.9 + - + +
256C ARG* 2.9 36.1 + - - -
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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