Contacts of the strand formed by residues 203 - 211 (chain C) in PDB entry 3Q2K
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 VAL 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C LEU* 4.4 10.1 - - + -
197C ASP* 4.3 5.2 + - + +
201C GLY 3.4 2.9 + - - +
202C PRO* 1.3 73.1 - - - +
204C GLU* 1.3 60.8 + - - +
205C SER 3.7 25.1 - - - +
206C VAL* 4.1 3.4 - - + -
227C LEU* 5.0 5.8 - - + -
228C ARG 3.8 6.5 - - - +
229C TRP* 3.6 27.4 - - + +
230C ARG* 3.7 8.1 + - - -
331C LEU* 3.7 36.8 - - + -
347C LEU* 3.2 35.2 - - + +
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Residues in contact with GLU 204 (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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202C PRO 3.8 1.8 + - - -
203C VAL* 1.3 72.6 - - - +
205C SER* 1.3 69.2 + - - +
228C ARG* 2.9 39.6 + - + +
229C TRP 4.0 6.7 - - - +
230C ARG* 3.9 41.5 + - + +
344C ARG* 4.9 8.3 + - - +
346C PRO* 3.4 2.8 - - + +
347C LEU* 2.7 28.3 + - - +
210G THR 5.2 5.2 - - - +
211G ALA* 5.9 2.8 - - - +
228H ARG* 5.6 4.1 + - - -
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Residues in contact with SER 205 (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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203C VAL* 3.7 5.3 - - - +
204C GLU* 1.3 87.8 + - - +
206C VAL* 1.3 69.1 + - - +
228C ARG* 3.1 28.4 + - - +
344C ARG* 3.5 29.4 + - - -
345C ILE 3.4 14.4 - - - -
346C PRO* 3.5 7.9 - - - -
347C LEU* 4.4 2.2 - - - +
209D TYR* 3.1 20.3 + - - -
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.1 1.8 - - + -
205C SER* 1.3 80.9 - - - +
207C TYR* 1.3 64.1 + - - +
225C ALA* 4.8 0.7 - - + -
226C ALA 3.2 9.2 - - - +
227C LEU* 3.7 20.9 - - + -
331C LEU* 4.0 23.8 - - + -
334C ALA* 3.8 17.9 - - + +
335C ILE* 3.8 39.5 - - + +
338C SER* 4.1 3.5 + - - -
344C ARG* 3.4 4.2 - - - +
345C ILE* 3.0 29.4 + - + +
347C LEU* 5.6 0.7 - - + -
209D TYR* 3.4 6.1 - - - -
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Residues in contact with TYR 207 (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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206C VAL* 1.3 75.8 - - - +
208C ALA* 1.3 79.9 + - - +
209C TYR* 3.9 24.5 - + - -
224C VAL 4.1 0.2 - - - +
225C ALA* 3.2 1.5 - - - -
226C ALA* 2.6 41.5 + - + +
338C SER* 3.4 3.1 - - - -
342C GLY* 3.6 15.9 - - - -
343C VAL* 3.6 37.7 - - - -
344C ARG* 3.6 0.9 - - - -
207D TYR* 3.2 64.4 - + + -
209D TYR* 3.6 0.8 + - - -
226D ALA* 4.7 2.4 - - + +
228D ARG* 5.5 0.5 + - - -
344D ARG* 3.3 36.6 + - + -
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Residues in contact with ALA 208 (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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207C TYR* 1.3 93.5 + - - +
209C TYR* 1.3 61.7 - - - +
210C THR* 4.7 0.9 - - + -
224C VAL 3.2 12.6 - - - +
225C ALA* 4.1 5.8 - - + -
335C ILE* 3.6 42.4 - - + +
338C SER* 2.8 15.5 + - - +
339C ALA* 3.4 20.0 - - + +
342C GLY* 5.7 0.2 - - - -
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Residues in contact with TYR 209 (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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207C TYR* 3.9 21.1 - + - -
208C ALA* 1.3 72.8 - - - +
210C THR* 1.3 65.5 + - - +
223C GLY* 3.3 1.4 - - - -
224C VAL* 3.0 34.9 + - + +
339C ALA* 4.6 1.3 - - - +
205D SER* 2.9 31.6 + - - -
206D VAL* 3.2 25.1 + - - -
207D TYR 3.5 0.6 + - - -
226D ALA* 3.6 31.2 - - + -
227D LEU 3.6 22.2 - - - -
228D ARG* 3.6 43.5 - - + +
234D MET* 3.6 18.3 - - + +
344D ARG* 3.6 9.4 - - - +
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Residues in contact with THR 210 (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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230B ARG* 4.9 5.4 + - - -
178C TRP* 5.5 3.5 - - - -
185C PHE* 3.9 27.1 - - + -
208C ALA* 4.7 1.6 - - + -
209C TYR* 1.3 80.8 - - - +
211C ALA* 1.3 65.7 + - - +
220C GLU* 3.6 24.7 + - + +
222C THR 3.5 5.2 - - - -
335C ILE* 4.6 10.5 - - + -
336C TYR* 5.1 4.6 - - + -
339C ALA* 3.4 29.3 + - + +
228D ARG* 4.7 9.8 + - - +
234D MET* 3.7 3.9 - - - +
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Residues in contact with ALA 211 (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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230B ARG* 4.1 8.3 - - - +
210C THR* 1.3 78.2 - - - +
212C THR* 1.3 61.3 + - - +
213C LEU* 3.6 17.3 - - + -
220C GLU* 3.4 5.4 - - - +
221C ASP* 3.1 19.8 + - - +
222C THR* 2.9 16.6 + - - +
228D ARG* 6.3 0.9 - - - +
232D GLY 4.9 1.3 - - - +
234D MET* 3.3 22.4 - - + -
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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