Contacts of the strand formed by residues 203 - 211 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196L LEU* 4.6 5.6 - - + +
197L ASP* 4.5 4.5 + - + +
201L GLY 4.3 2.2 - - - +
202L PRO* 1.3 74.6 - - - +
204L GLU* 1.3 64.2 + - - +
205L SER 3.7 11.4 - - - +
206L VAL* 3.7 30.3 - - + -
227L LEU* 4.7 5.4 - - + -
228L ARG 3.7 11.2 - - - +
229L TRP* 3.7 28.5 - - + +
230L ARG* 3.8 8.9 + - - -
331L LEU* 4.1 24.2 - - + -
347L LEU* 3.8 30.1 - - + +
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Residues in contact with GLU 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J ARG* 5.9 0.7 + - - -
202L PRO 3.7 1.8 + - - -
203L VAL* 1.3 74.8 - - - +
205L SER* 1.3 70.3 + - - +
228L ARG* 2.8 58.9 + - - +
229L TRP 4.1 2.7 - - - +
230L ARG* 4.0 40.3 - - + +
344L ARG* 3.5 11.1 + - - +
346L PRO* 3.5 3.2 - - + +
347L LEU* 3.0 26.9 + - - +
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Residues in contact with SER 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K TYR* 2.7 21.0 + - - -
203L VAL* 3.7 3.2 - - - +
204L GLU* 1.3 93.3 + - - +
206L VAL* 1.3 70.5 + - - +
228L ARG* 3.2 24.3 + - - -
344L ARG* 2.7 33.4 + - - -
345L ILE 3.4 12.8 - - - -
346L PRO* 3.9 1.8 - - - -
347L LEU* 4.6 2.2 - - - +
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Residues in contact with VAL 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K TYR* 3.4 7.1 + - - -
203L VAL* 3.7 19.3 - - + -
205L SER* 1.3 79.5 - - - +
207L TYR* 1.3 65.1 + - - +
208L ALA* 5.1 0.2 - - + -
225L ALA* 5.0 0.7 - - + -
226L ALA 3.4 11.2 - - - +
227L LEU* 3.7 16.4 - - + -
331L LEU* 3.8 15.0 - - + -
334L ALA* 3.9 15.0 - - + +
335L ILE* 3.8 37.9 - - + +
338L SER* 4.0 1.9 + - - -
344L ARG* 3.5 2.6 - - - -
345L ILE 2.9 33.6 + - - +
347L LEU* 5.0 2.0 - - + -
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Residues in contact with TYR 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K TYR* 3.4 61.7 - + + -
209K TYR* 3.7 1.6 + - - +
226K ALA* 4.7 2.9 - - + +
344K ARG* 2.9 37.3 - - + +
206L VAL* 1.3 77.9 - - - +
208L ALA* 1.3 76.6 + - - +
209L TYR* 3.8 24.7 - + - -
225L ALA* 3.3 1.3 - - - -
226L ALA* 2.7 39.6 + - + +
338L SER* 3.3 3.6 - - - -
342L GLY* 3.4 32.6 + - - -
343L VAL* 3.6 11.2 - - - -
344L ARG 3.5 16.8 - - - -
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Residues in contact with ALA 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L TYR* 1.3 90.8 - - - +
209L TYR* 1.3 65.0 + - - +
210L THR* 4.6 0.9 - - + -
224L VAL 3.2 13.5 - - - +
225L ALA* 4.0 5.2 - - + -
335L ILE* 3.6 45.1 - - + +
338L SER* 2.9 10.0 + - - +
339L ALA* 3.3 20.6 + - + +
342L GLY* 5.6 0.2 - - - -
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Residues in contact with TYR 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K SER* 2.8 22.9 + - - -
206K VAL 3.4 21.8 + - - -
207K TYR 4.3 0.9 - - - -
226K ALA* 3.7 39.9 - - + -
227K LEU 3.8 14.4 - - - -
228K ARG* 3.5 48.9 - - + +
234K MET* 3.7 19.3 - - + -
344K ARG* 3.6 10.3 - - - +
207L TYR* 3.8 19.7 - + - -
208L ALA* 1.3 75.4 - - - +
210L THR* 1.3 63.7 + - - +
223L GLY* 3.1 2.1 - - - -
224L VAL* 2.9 35.2 + - + +
339L ALA* 4.5 2.2 - - - +
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Residues in contact with THR 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ARG* 4.7 8.9 + - - +
234K MET* 3.7 5.9 - - - +
178L TRP* 5.6 3.8 - - - -
185L PHE* 4.2 17.3 - - + -
208L ALA* 4.6 7.0 - - + -
209L TYR* 1.3 79.3 - - - +
211L ALA* 1.3 65.8 + - - +
220L GLU* 3.6 26.0 + - + +
222L THR 3.4 7.9 - - - -
223L GLY* 4.1 7.4 - - - -
335L ILE* 4.7 4.9 - - + -
336L TYR* 5.2 3.8 - - + -
339L ALA* 3.4 28.9 + - + +
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Residues in contact with ALA 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ARG* 6.0 1.8 - - - +
232K GLY 5.3 0.7 - - - +
234K MET* 3.9 11.2 - - + +
210L THR* 1.3 78.6 + - - +
212L THR* 1.3 63.6 + - - +
213L LEU* 3.6 24.9 - - + -
220L GLU* 3.3 5.1 - - - -
221L ASP* 2.9 27.0 + - - +
222L THR* 2.9 12.3 + - - +
230N ARG 5.6 3.8 - - - +
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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