Contacts of the strand formed by residues 156 - 162 (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 PHE 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A VAL* 3.7 38.4 - - + +
149A ALA* 5.3 0.9 - - + -
150A TYR* 3.6 37.2 - + + -
154A LYS 4.8 0.4 - - - -
155A PRO* 1.3 77.7 - - - +
157A TYR* 1.3 72.6 + - - +
158A LEU* 4.4 6.3 - - + -
187A PHE* 3.8 32.5 - + + -
189A VAL* 3.3 28.6 - - + +
190A PRO* 3.2 22.0 - - - +
303A ILE* 3.6 8.7 - - - -
304A GLN* 3.3 28.7 - - + +
306A LEU* 4.2 17.5 - - + -
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Residues in contact with TYR 157 (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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156A PHE* 1.3 81.2 - - - +
158A LEU* 1.3 71.2 + - - +
159A TYR* 4.4 5.6 - - + -
189A VAL* 4.3 0.7 - - - -
190A PRO* 3.3 28.0 - - + +
192A VAL* 4.4 8.3 - - + -
287A PRO 2.5 28.6 + - - -
288A SER 2.9 17.5 - - - -
289A PHE 3.1 7.3 + - - -
290A SER* 3.9 13.5 - - - -
293A PHE* 4.2 14.4 - + - -
297A PHE* 3.7 27.1 - + + -
303A ILE* 3.7 16.4 - - + -
304A GLN 2.9 16.2 + - - +
305A CYS* 3.3 31.1 - - + -
306A LEU 2.8 23.7 + - - -
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Residues in contact with LEU 158 (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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156A PHE* 4.4 4.5 - - + -
157A TYR* 1.3 78.4 - - - +
159A TYR* 1.3 62.5 + - - +
180A THR* 4.0 16.8 - - + +
183A LEU* 4.1 19.3 - - + -
184A GLN* 3.8 29.8 - - + +
189A VAL* 3.6 25.1 - - + -
190A PRO 2.7 11.9 + - - +
191A LEU* 3.3 14.2 - - + +
192A VAL* 2.7 28.4 + - - +
305A CYS* 4.5 0.2 - - - -
306A LEU* 3.2 43.5 - - + +
308A PRO* 4.5 4.9 - - + -
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Residues in contact with TYR 159 (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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157A TYR* 4.4 2.0 - - + -
158A LEU* 1.3 78.5 - - - +
160A THR* 1.3 82.4 + - - +
161A GLY* 4.8 3.2 + - - -
192A VAL* 3.2 32.3 - - + -
194A GLN* 2.8 31.5 + - + +
284A GLN* 3.2 21.1 + - - +
287A PRO* 3.4 27.6 - - + -
288A SER* 4.0 11.2 - - - -
305A CYS* 3.6 16.4 - - - -
306A LEU 3.0 7.3 + - - -
307A ILE* 3.6 52.0 - - + +
308A PRO* 4.4 1.2 - - - +
317A PHE* 4.9 7.7 - + - -
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Residues in contact with THR 160 (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* 1.3 84.0 - - - +
161A GLY* 1.3 65.9 + - - +
176A PRO* 4.7 14.6 - - + -
177A PHE* 5.3 12.0 - - + -
180A THR* 3.7 32.1 + - - +
191A LEU* 3.8 5.2 - - - +
192A VAL 3.0 5.1 + - - +
193A ILE* 3.1 14.2 - - - +
194A GLN 2.9 20.6 + - - -
307A ILE* 5.5 2.2 - - + -
308A PRO* 3.7 23.6 - - + +
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Residues in contact with GLY 161 (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* 4.4 5.7 + - - -
160A THR* 1.3 81.8 - - - +
162A ARG* 1.3 63.6 + - - +
177A PHE* 3.9 14.4 - - - -
193A ILE* 4.7 2.9 - - - -
194A GLN* 3.1 19.5 - - - -
196A THR* 5.7 1.6 - - - -
284A GLN* 5.9 1.6 - - - -
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Residues in contact with ARG 162 (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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161A GLY* 1.3 76.3 - - - +
163A GLY* 1.3 71.0 + - - +
164A PRO* 2.9 14.4 - - - +
165A SER* 4.3 17.4 + - - -
167A GLU 5.7 1.8 + - - -
169A MET* 3.7 38.2 - - - +
173A HIS* 3.3 34.8 + - - -
177A PHE* 3.9 21.8 - - + -
193A ILE* 5.6 0.2 - - + -
194A GLN 3.0 6.2 + - - +
195A MET* 3.7 29.3 - - + -
196A THR* 3.4 16.9 + - - +
218A ASN* 2.8 27.4 + - - +
222A ILE* 4.1 7.6 - - + -
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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