Contacts of the strand formed by residues 196 - 202 (chain A) in PDB entry 1UK0
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 ARG 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.2 22.8 + - - +
190A PHE 3.3 24.5 + - - -
191A LYS* 3.1 32.0 + - - +
192A GLN* 4.9 1.4 - - - +
193A LEU 3.0 26.2 + - - -
194A HIS* 3.3 2.2 + - - +
195A ASN* 1.4 70.9 - - - +
197A ARG* 1.4 52.5 + - - +
262A GLU* 3.6 14.9 + - - -
263A VAL 3.2 3.4 - - - +
264A ALA* 3.5 15.9 - - - -
304A ASP 4.5 11.3 + - - -
305A GLY 3.7 22.0 + - - +
306A VAL* 3.2 13.6 - - + +
307A ASP* 2.6 35.4 + - - +
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Residues in contact with ARG 197 (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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195A ASN* 3.5 20.6 + - - +
196A ARG* 1.4 73.4 - - - +
198A LEU* 1.3 62.1 + - - +
199A LEU* 3.3 31.9 + - + +
238A ASP* 5.9 0.4 - - - -
261A GLY 3.3 1.2 - - - +
263A VAL* 2.7 32.7 + - - +
265A LEU* 3.4 18.2 - - + +
268A MET* 4.0 17.6 - - - +
288A LYS* 5.8 1.6 - - - +
300A ASN* 5.1 2.4 + - - +
306A VAL* 3.5 5.8 - - - +
307A ASP* 3.2 29.0 + - - +
309A PRO* 4.5 15.3 - - - +
328A TYR* 3.3 32.5 - - - -
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Residues in contact with LEU 198 (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 TYR* 2.8 22.7 + - + -
197A ARG* 1.3 69.1 - - - +
199A LEU* 1.3 67.2 + - - +
260A LEU* 3.8 30.3 - - + +
261A GLY 3.2 18.2 - - - +
262A GLU* 4.1 4.7 - - + +
303A LEU* 4.7 9.0 - - + -
306A VAL* 4.2 5.8 - - + +
307A ASP 2.9 10.1 + - - -
308A VAL* 3.9 38.4 - - + -
309A PRO* 3.6 3.1 - - - +
339A LYS* 3.8 28.7 - - + -
340A TYR* 4.4 17.9 - - + -
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Residues in contact with LEU 199 (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 TYR* 4.0 1.3 - - - -
197A ARG* 3.7 29.2 - - + -
198A LEU* 1.3 85.4 - - - +
200A TRP* 1.3 65.7 + - - +
201A HIS 3.4 0.3 + - - -
236A PHE* 4.0 14.6 - - + -
237A ALA 3.3 15.9 - - - +
238A ASP* 3.9 11.7 - - + -
260A LEU* 3.5 5.7 - - - -
261A GLY* 2.7 37.5 + - - +
263A VAL* 3.8 27.1 - - + -
265A LEU* 4.5 0.9 - - + -
309A PRO* 4.1 2.2 - - + -
328A TYR* 3.6 45.8 - - + -
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Residues in contact with TRP 200 (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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153A ILE 4.4 1.6 - - - -
156A TYR* 3.2 64.6 - + - -
157A VAL* 3.2 24.7 - - + -
199A LEU* 1.3 72.5 - - - +
201A HIS* 1.3 57.7 + - - +
236A PHE* 3.5 6.1 - - - -
237A ALA 2.8 48.0 + - - +
238A ASP 3.7 8.0 + - - -
239A MET 3.9 1.8 - - - -
240A VAL* 3.3 29.2 - - + +
243A SER* 3.2 23.4 + - - +
258A ILE* 3.2 29.8 - - + -
259A LEU 3.4 8.1 - - - +
260A LEU* 3.5 31.2 - - + -
342A LEU* 3.6 22.0 - - + -
501A FRM 4.2 0.3 - - - +
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Residues in contact with HIS 201 (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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199A LEU 3.4 3.2 + - - -
200A TRP* 1.3 71.0 - - - +
202A GLY* 1.3 57.7 + - - +
203A SER* 3.6 12.0 + - - -
208A PHE* 4.5 0.3 - - - -
216A LEU* 3.6 41.4 - - + +
234A ILE* 5.3 3.4 - - + -
235A TYR 2.8 30.7 + - - -
236A PHE* 3.7 18.8 - - + -
258A ILE* 4.9 0.2 - - - -
259A LEU* 3.1 43.8 + - + +
501A FRM 3.2 52.3 + + + +
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Residues in contact with GLY 202 (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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201A HIS* 1.3 67.0 - - - +
203A SER* 1.3 63.7 + - - -
243A SER* 3.3 30.7 - - - -
246A TYR* 3.2 8.9 - - - +
247A CYS* 5.3 0.2 - - - -
258A ILE* 4.3 13.7 - - - +
501A FRM 2.5 47.6 + - - +
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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