Contacts of the strand formed by residues 159 - 167 (chain A) in PDB entry 3UJK
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 HIS 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS 5.6 0.2 - - - -
109A CYS* 2.7 32.4 + - - -
110A VAL 4.1 0.2 - - - -
111A PRO* 3.6 31.2 - - + +
132A ILE 3.7 2.9 - - - -
133A PRO* 3.4 14.1 - - + -
134A ARG* 3.1 36.6 + - - +
135A PHE* 4.1 2.2 - - - -
157A SER* 3.2 18.4 + - - -
158A ALA* 1.3 72.3 - - - +
160A PHE* 1.3 59.7 + - - +
161A PHE* 3.7 24.2 - - + -
237A ALA 3.7 0.9 - - - +
238A VAL* 3.3 6.8 - - - +
239A VAL* 2.9 43.6 + - + +
240A PHE 6.5 0.4 - - - -
241A PRO* 6.4 0.4 - - + -
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Residues in contact with PHE 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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130A SER* 3.9 19.3 - - - -
131A THR* 3.6 0.5 - - - -
132A ILE* 2.9 41.8 + - + +
135A PHE* 3.6 29.1 - + + -
159A HIS* 1.3 71.6 - - - +
161A PHE* 1.3 70.5 + - - +
162A GLY 4.0 7.2 - - - -
164A TYR* 3.3 27.6 - - - -
180A MET* 3.9 7.2 - - + -
181A HIS* 3.7 39.9 - + + -
184A LEU* 3.7 25.6 - - + -
236A VAL* 3.4 29.4 - - + -
237A ALA 3.7 2.2 - - - -
238A VAL* 4.5 2.9 - - + +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO* 5.1 3.8 - - + -
112A LEU 6.0 0.2 - - - -
113A TYR* 3.7 40.4 - + + -
130A SER 3.3 3.8 - - - +
131A THR* 4.0 12.6 - - + -
132A ILE 4.8 2.5 - - - -
133A PRO 5.8 0.2 - - - -
159A HIS* 3.7 32.1 - + + -
160A PHE* 1.3 82.8 - - - +
162A GLY* 1.3 58.4 + - - +
236A VAL* 3.2 5.5 - - - +
237A ALA* 2.8 43.6 + - + +
239A VAL* 3.9 24.0 - - + -
334A LEU* 3.7 14.6 - - + +
407A VAL* 3.8 26.0 - - + -
409A VAL* 3.8 27.8 - - + -
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Residues in contact with GLY 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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129A VAL* 3.3 4.9 - - - +
130A SER 2.9 34.8 + - - +
160A PHE* 4.0 2.7 - - - -
161A PHE* 1.3 75.1 - - - +
163A VAL* 1.3 68.4 + - - +
164A TYR* 3.7 23.6 - - - -
235A VAL 3.3 8.3 - - - -
236A VAL* 4.3 0.9 - - - -
334A LEU* 4.6 0.2 - - - -
407A VAL* 4.7 1.1 - - - +
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Residues in contact with VAL 163 (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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127A ASP* 5.4 0.2 - - - +
128A SER 3.7 4.3 - - - +
129A VAL* 4.3 6.5 - - + -
162A GLY* 1.3 77.7 - - - +
164A TYR* 1.3 70.1 + - - +
233A THR* 4.3 2.5 + - - -
234A SER* 3.6 0.9 - - - -
235A VAL* 2.9 41.9 + - + +
252A SER* 4.4 4.3 - - - +
334A LEU* 4.0 25.8 - - + +
335A ALA* 4.1 2.0 - - - -
336A SER* 3.8 31.4 - - - +
405A SER* 4.1 17.7 - - - +
407A VAL* 4.0 22.0 - - + +
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Residues in contact with TYR 164 (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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127A ASP* 3.3 4.7 - - - +
128A SER 2.8 51.4 + - - +
130A SER* 3.7 19.9 + - - -
160A PHE* 3.3 34.7 - - - -
162A GLY* 3.7 16.4 - - - -
163A VAL* 1.3 84.1 - - - +
165A ASP* 1.3 60.9 + - - +
166A GLY 3.8 0.2 - - - -
173A ALA* 3.7 15.5 - - + +
176A CYS* 3.5 24.0 + - + -
177A ARG* 3.7 20.0 - - - -
180A MET* 3.5 11.5 - - + +
181A HIS* 5.4 0.2 + - - -
232A SER* 3.5 12.6 - - - +
233A THR 3.4 8.1 - - - -
234A SER* 3.4 25.8 - - - -
236A VAL* 3.9 6.5 - - + +
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Residues in contact with ASP 165 (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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127A ASP* 3.1 19.0 - - - +
163A VAL 4.1 0.2 - - - -
164A TYR* 1.3 69.5 - - - +
166A GLY* 1.3 59.9 + - - +
167A HIS* 4.1 3.1 + - - -
232A SER* 3.3 3.5 + - - -
233A THR* 2.9 44.2 + - + +
251A ASP* 4.4 0.7 - - - +
252A SER* 3.6 9.8 + - - +
336A SER* 3.9 7.8 - - - -
337A ASP* 3.0 8.0 + - - +
424A MG 2.3 25.8 - - - -
425A MG 2.9 18.5 - - - -
426A MG 2.3 30.6 - - - -
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Residues in contact with GLY 166 (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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126A GLU* 2.8 28.4 + - - +
164A TYR 3.7 0.4 + - - -
165A ASP* 1.3 74.7 + - - +
167A HIS* 1.3 59.0 + - - +
169A GLY 3.9 9.0 - - - -
173A ALA* 3.8 6.0 - - - +
231A GLY 3.2 10.8 - - - -
232A SER* 3.7 8.1 + - - -
426A MG 2.2 33.1 - - - -
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Residues in contact with HIS 167 (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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126A GLU* 3.7 4.3 - - - -
165A ASP 4.1 4.0 + - - -
166A GLY* 1.3 76.9 - - - +
168A GLY* 1.3 61.0 + - - +
169A GLY 3.1 6.6 + - - -
229A THR 4.8 2.2 - - - -
230A VAL* 3.4 1.9 - - - +
231A GLY* 2.8 49.0 + - - +
232A SER* 3.7 6.5 - - - -
299A LEU* 3.8 19.6 - - + +
301A MET* 3.8 36.7 - - + +
304A SER* 4.1 1.3 - - - -
307A ASP* 2.6 41.1 + - - -
309A TYR* 6.1 0.2 - - - -
426A MG 4.4 0.2 - - - -
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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