Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 2QUK
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 LEU 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.3 27.4 - - + +
160A THR* 3.8 9.4 - - - +
180A THR* 3.5 27.4 - - + -
184A GLN* 3.4 19.5 - - - +
189A VAL 3.8 0.2 + - - -
190A PRO* 1.3 74.7 - - - +
192A VAL* 1.3 65.7 + - - +
193A ILE* 3.7 21.8 - - + -
227A PHE* 3.4 40.2 - - + -
231A LYS 2.8 8.7 + - - +
232A THR* 3.2 4.6 - - - +
233A PHE* 2.7 34.1 + - - +
466A LEU* 4.9 1.6 - - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 4.4 9.9 - - + -
158A LEU 2.7 11.7 + - - +
159A TYR* 3.2 27.7 - - + -
160A THR 3.0 23.4 + - - +
191A LEU* 1.3 75.7 - - - +
193A ILE* 1.3 61.9 + - - +
233A PHE* 3.4 21.3 - - + -
235A PHE* 3.9 4.9 - - + -
293A PHE* 3.5 53.8 - - + -
296A ILE* 4.4 8.5 - - + -
297A PHE* 5.9 0.2 - - + -
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Residues in contact with ILE 193 (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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160A THR* 3.1 15.3 - - - +
161A GLY* 4.7 2.5 - - - -
177A PHE* 4.9 6.5 - - + -
191A LEU* 3.7 24.9 - - + -
192A VAL* 1.3 77.9 - - - +
194A GLN* 1.3 62.9 + - - +
195A MET* 4.1 21.3 - - - -
222A ILE* 3.9 28.0 - - + -
227A PHE* 4.7 5.6 - - + -
232A THR* 3.6 14.6 - - - +
233A PHE 2.6 13.3 + - - +
234A ILE* 3.6 27.8 - - + +
235A PHE* 2.8 35.8 + - - +
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Residues in contact with GLN 194 (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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159A TYR* 2.8 37.6 + - + -
160A THR 2.9 10.0 + - - +
161A GLY* 3.1 3.1 - - - -
162A ARG 3.0 28.4 + - - +
192A VAL 4.2 0.2 - - - -
193A ILE* 1.3 70.9 - - - +
195A MET* 1.3 65.1 + - - +
196A THR* 3.6 17.9 + - + +
235A PHE* 3.4 26.3 - - + -
237A ASP* 2.7 31.3 + - - +
247A PHE* 4.0 2.4 - - - -
280A PHE* 5.6 0.2 - - - -
283A ILE* 3.1 22.2 + - - +
284A GLN* 3.6 17.1 - - - +
287A PRO* 3.7 7.2 - - - +
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Residues in contact with MET 195 (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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162A ARG* 3.7 22.4 - - + -
164A PRO* 4.0 11.0 - - + -
193A ILE* 4.1 7.9 - - - -
194A GLN* 1.3 81.0 - - - +
196A THR* 1.3 51.4 + - - +
197A ASP* 2.7 28.7 + - - +
215A ALA* 3.6 38.8 - - + +
218A ASN* 3.6 25.1 - - + -
219A ALA* 5.1 0.2 - - - -
222A ILE* 3.8 22.0 - - + -
234A ILE* 3.7 19.7 - - + -
235A PHE 2.7 23.7 + - - +
236A SER* 4.0 3.1 - - - -
237A ASP 3.2 10.5 + - - -
461A MET* 5.7 1.8 - - - -
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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