Contacts of the strand formed by residues 336 - 347 (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 VAL 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 3.3 7.7 - - - +
186A ARG* 2.7 29.8 + - - +
187A TYR* 3.9 4.5 - - - +
216A LEU* 4.6 13.7 - - + +
234A ILE* 4.3 9.9 - - + -
236A PHE* 3.4 38.6 - - + -
261A GLY* 5.7 0.7 - - - -
262A GLU 3.7 2.0 - - - +
263A VAL* 3.7 13.2 - - + -
330A VAL* 4.1 12.1 - - + -
333A ILE 3.0 7.9 + - - +
334A ALA 2.8 9.8 + - - +
335A GLN* 1.4 76.5 - - - +
337A ASN* 1.3 71.9 + - - +
338A LEU* 4.3 20.4 - - + +
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Residues in contact with ASN 337 (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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183A GLU* 2.9 40.4 + - - +
184A CYS* 5.0 3.8 - - - +
187A TYR* 3.8 25.0 - - + -
191A LYS* 5.6 2.6 + - - -
261A GLY* 3.6 0.6 - - - -
262A GLU* 2.8 46.4 + - + +
336A VAL* 1.3 83.4 + - - +
338A LEU* 1.3 70.0 + - - +
339A LYS* 3.4 27.6 + - - +
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Residues in contact with LEU 338 (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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178A ILE* 3.1 32.8 - - + +
179A GLU* 5.2 0.7 - - - -
180A ARG* 4.3 18.6 + - + -
183A GLU* 2.7 20.4 + - - +
211A ILE* 3.9 33.7 - - + +
212A LEU* 5.5 2.5 - - + -
216A LEU* 3.7 33.0 - - + +
259A LEU* 3.9 28.3 - - + -
260A LEU 4.6 0.9 - - - -
261A GLY* 4.7 7.4 - - - -
336A VAL* 4.2 10.1 - - + -
337A ASN* 1.3 77.7 + - - +
339A LYS* 1.4 65.4 + - - +
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Residues in contact with LYS 339 (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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177A LYS* 3.6 14.4 - - + +
178A ILE* 2.9 33.7 + - - +
198A LEU* 3.8 13.9 - - + -
260A LEU 3.1 12.4 + - - +
262A GLU* 3.4 44.8 + - + +
303A LEU* 6.6 0.2 - - - -
306A VAL* 6.3 0.4 - - - -
337A ASN* 3.5 26.5 + - - +
338A LEU* 1.4 77.2 + - - +
340A TYR* 1.3 82.8 + - + +
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Residues in contact with TYR 340 (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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143A VAL* 4.5 3.6 - - + -
149A GLU* 2.8 36.9 + - - -
153A ILE* 4.1 22.0 - - + -
175A ILE* 5.6 0.2 - - + -
176A PHE 3.4 10.8 - - - +
177A LYS* 4.0 25.6 - - + +
178A ILE* 4.3 4.9 - - - -
198A LEU* 4.4 16.6 - - + -
259A LEU* 3.5 9.0 - - - +
260A LEU* 2.8 56.8 + - + +
303A LEU* 5.4 10.3 - - + +
339A LYS* 1.3 96.6 + - + +
341A LEU* 1.3 58.2 + - - +
342A LEU* 4.1 14.4 - - + -
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Residues in contact with LEU 341 (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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11A LEU* 3.9 26.7 - - + -
140A ILE* 5.8 0.9 - - + -
175A ILE* 3.5 1.7 - - - +
176A PHE* 2.6 52.4 + - + +
178A ILE* 4.2 13.4 - - + +
208A PHE* 3.9 12.3 - - + -
212A LEU* 4.4 19.3 - - + -
257A LEU* 3.6 33.4 - - + -
258A ILE 3.4 23.1 - - - +
259A LEU* 4.2 10.3 - - + -
339A LYS 4.1 0.4 + - - -
340A TYR* 1.3 71.7 - - - +
342A LEU* 1.4 79.8 + - - +
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Residues in contact with LEU 342 (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* 3.9 23.6 - - + -
157A VAL* 3.7 20.4 - - + -
172A VAL* 4.3 17.7 - - + -
174A ASP 3.4 7.6 - - - +
175A ILE* 4.4 7.2 - - + -
176A PHE* 4.7 0.4 - - - +
200A TRP* 3.6 28.5 - - + -
240A VAL* 5.8 0.2 - - + -
257A LEU* 3.7 4.3 - - - -
258A ILE* 3.2 29.7 + - + +
260A LEU* 4.4 4.9 - - + -
340A TYR* 4.1 15.3 - - + +
341A LEU* 1.4 104.4 - - - +
343A LYS* 1.3 59.3 + - - +
344A LEU* 3.4 23.3 + - + +
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Residues in contact with LYS 343 (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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7A PRO* 4.9 2.2 - - - +
10A ASP* 4.1 23.8 - - - +
11A LEU* 5.1 2.9 - - + +
14A MET* 3.6 35.3 - - + +
171A GLU 3.4 1.0 - - - +
172A VAL* 3.7 1.6 - - - +
173A ILE* 2.7 64.0 + - + +
174A ASP* 2.9 42.5 + - + +
176A PHE* 4.7 9.3 - - + -
255A ILE* 4.7 8.1 - - + -
256A GLY 4.3 2.0 - - - +
257A LEU* 4.4 7.4 - - + -
342A LEU* 1.3 71.2 - - - +
344A LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 344 (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 VAL* 4.1 14.4 - - + -
170A LEU* 3.5 34.3 - - + -
171A GLU 3.8 15.5 - - - +
172A VAL* 4.7 5.8 - - + -
173A ILE* 3.8 2.9 - - - +
240A VAL* 5.7 2.0 - - + -
255A ILE* 3.1 13.0 - - - +
256A GLY 2.9 45.4 + - - +
258A ILE* 4.2 17.7 - - + -
342A LEU* 3.4 40.4 - - + +
343A LYS* 1.3 75.8 - - - +
345A LYS* 1.3 59.1 + - - +
346A PHE* 3.4 17.5 - - + -
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Residues in contact with LYS 345 (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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170A LEU* 3.8 4.7 - - - +
171A GLU* 2.6 74.3 + - - +
173A ILE* 3.7 18.8 - - + +
254A PRO* 3.7 4.5 - - + +
255A ILE* 3.9 14.8 - - + -
344A LEU* 1.3 73.9 - - - +
346A PHE* 1.3 73.4 + - - +
347A ASN* 2.8 39.3 + - - +
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Residues in contact with PHE 346 (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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168A TYR* 3.3 52.7 - + - -
169A ASP 4.4 2.5 - - - -
170A LEU* 3.7 8.3 - - + -
244A ALA* 3.7 15.5 - - + -
245A ASN* 5.4 0.4 - - - -
247A CYS* 3.4 32.8 - - - -
249A THR* 2.6 35.9 - - + +
254A PRO* 2.7 28.2 + - - +
256A GLY 4.2 3.8 - - - -
258A ILE* 5.3 0.9 - - + -
344A LEU* 3.9 21.5 - - + -
345A LYS* 1.3 94.6 + - - +
347A ASN* 1.3 57.0 + - - +
348A PHE* 3.4 23.3 - + + -
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Residues in contact with ASN 347 (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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168A TYR* 3.4 1.2 - - - +
169A ASP* 2.8 45.8 + - + +
171A GLU* 3.0 16.9 + - + +
345A LYS* 2.8 31.2 + - - +
346A PHE* 1.3 69.7 - - - +
348A PHE* 1.3 64.9 + - - +
349A LYS 3.0 4.8 + - - -
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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