Contacts of the strand formed by residues 195 - 203 (chain C) in PDB entry 1QD6
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 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C VAL* 6.0 5.6 - - + -
174C LYS 3.2 12.8 - - - +
175C PRO* 3.8 12.6 - - + -
176C TRP* 3.5 9.6 - - - -
192C MET 4.1 1.0 - - - +
193C GLY* 5.4 0.2 - - - -
194C TYR* 1.3 88.1 - - + +
196C GLN* 1.3 71.1 + - - +
197C LEU* 4.1 22.4 - - + -
212C GLY 4.9 2.2 - - - -
213C GLN* 3.4 22.1 - - - +
214C TYR* 3.3 44.4 + - - +
216C TRP* 3.3 40.3 + + - -
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Residues in contact with GLN 196 (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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172C GLU* 3.7 3.7 + - - +
173C VAL* 3.6 2.6 - - - -
174C LYS* 2.9 51.6 + - + +
176C TRP* 3.6 18.8 - - + -
195C TYR* 1.3 79.7 - - - +
197C LEU* 1.3 66.8 + - - +
198C LYS* 4.0 19.5 - - - +
211C LYS* 3.4 37.2 - - + +
212C GLY 3.3 11.7 - - - +
213C GLN* 3.9 18.1 + - + +
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Residues in contact with LEU 197 (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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171C VAL* 3.9 17.3 - - + -
172C GLU 3.5 14.6 - - - +
173C VAL* 3.6 21.1 - - + -
195C TYR* 4.1 18.7 - - + -
196C GLN* 1.3 74.9 - - - +
198C LYS* 1.3 63.9 + - - +
199C ILE* 4.4 21.5 - - + -
210C ALA 3.8 0.9 - - - +
211C LYS* 3.3 3.1 - - - -
212C GLY* 2.8 40.1 + - - +
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Residues in contact with LYS 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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18A ILE* 6.2 1.6 - - - +
36C ASP* 3.9 25.3 + - - +
161C ARG* 5.7 0.2 - - - +
170C LEU* 4.5 2.9 - - + -
171C VAL* 3.3 5.5 - - - +
172C GLU* 2.8 80.9 + - + +
196C GLN* 4.0 20.5 - - - +
197C LEU* 1.3 74.7 - - - +
199C ILE* 1.3 66.2 + - - +
200C GLY 4.3 0.2 - - - -
209C SER* 6.1 0.2 - - - -
210C ALA 3.3 8.5 - - - +
211C LYS* 4.3 18.8 - - + -
268C LEU* 3.7 34.5 - - + +
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Residues in contact with ILE 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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169C TRP* 3.6 34.8 - - + -
170C LEU 3.4 5.8 - - - +
171C VAL* 4.4 12.8 - - + -
197C LEU* 4.4 23.3 - - + -
198C LYS* 1.3 79.9 - - - +
200C GLY* 1.3 63.1 + - - +
208C LEU 3.9 0.3 - - - +
209C SER* 3.3 5.0 - - - -
210C ALA* 2.8 54.0 + - + +
268C LEU* 4.3 3.4 - - - -
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Residues in contact with GLY 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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169C TRP* 3.5 9.4 - - - -
170C LEU* 2.8 34.8 + - - +
198C LYS 4.3 0.2 - - - -
199C ILE* 1.3 75.5 - - - +
201C TYR* 1.3 61.2 + - - +
208C LEU 3.4 6.1 - - - -
268C LEU* 4.0 15.6 - - - +
269C PHE* 3.6 18.8 - - - -
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Residues in contact with TYR 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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168C ASN* 3.3 37.2 + - + -
169C TRP* 3.3 53.4 - + + -
199C ILE* 5.9 0.2 - - + -
200C GLY* 1.3 73.7 - - - +
202C HIS* 1.3 65.7 + - - +
203C LEU* 3.5 35.5 + - + +
207C VAL* 3.4 3.6 - - - -
208C LEU* 2.8 55.7 + - + +
269C PHE* 3.7 4.8 - - - -
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Residues in contact with HIS 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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15A ARG* 3.6 39.1 + - - +
168C ASN* 2.8 40.3 + - + +
201C TYR* 1.3 73.4 - - - +
203C LEU* 1.3 60.9 + - - +
204C GLY 2.7 30.6 + - - +
205C ASP* 3.8 16.8 - - - -
206C ALA 3.3 5.4 + - - -
207C VAL* 3.8 13.2 - - + -
236C ARG* 5.6 1.8 + - - -
269C PHE* 3.3 51.3 + + + -
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Residues in contact with LEU 203 (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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201C TYR* 3.5 26.3 + - + +
202C HIS* 1.3 70.7 - - - +
204C GLY* 1.3 59.3 + - - +
205C ASP 3.3 0.2 + - - -
206C ALA* 2.9 35.1 + - + +
208C LEU* 4.1 24.0 - - + -
229C TYR* 5.1 0.9 - - - -
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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