Contacts of the strand formed by residues 336 - 344 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B GLU* 3.1 18.1 - - - +
186B ARG* 3.8 5.4 + - - +
187B TYR* 3.3 18.4 + - - +
216B LEU* 4.9 12.6 - - + +
234B ILE* 4.3 16.2 - - + -
236B PHE* 4.0 31.2 - - + -
261B GLY* 5.2 2.9 - - - -
262B GLU 3.6 10.8 - - - +
263B VAL* 4.4 3.1 - - + -
330B VAL* 4.5 6.1 - - + -
333B ILE 3.5 11.3 + - - +
334B ALA 3.1 1.5 + - - +
335B GLN* 1.3 87.6 - - - +
337B ASN* 1.3 71.5 + - - +
338B LEU* 4.5 15.9 - - + +
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Residues in contact with ASN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B GLU* 6.0 1.7 - - - +
183B GLU* 3.6 7.9 - - - +
184B CYS* 3.4 31.0 + - - +
187B TYR* 2.9 46.5 - - + -
191B LYS* 5.2 0.2 - - - +
261B GLY* 3.9 2.1 - - - -
262B GLU* 3.1 40.8 + - + +
336B VAL* 1.3 74.4 - - - +
338B LEU* 1.3 79.9 + - - +
339B LYS* 3.1 16.5 + - - +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 2.9 33.0 - - + +
180B ARG* 4.2 19.9 + - + +
183B GLU* 2.8 20.2 + - - +
211B ILE* 4.1 25.6 - - + +
212B LEU* 4.6 7.2 - - + -
215B GLY* 4.4 7.2 - - - -
216B LEU* 4.8 6.7 - - + +
259B LEU* 3.3 49.6 - - + -
260B LEU 3.8 8.3 - - - +
261B GLY* 4.9 2.9 - - - -
336B VAL* 4.6 11.4 - - + -
337B ASN* 1.3 83.1 + - - +
339B LYS* 1.4 60.0 + - - +
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LYS* 3.7 11.5 - - + +
178B ILE* 2.9 26.5 + - - +
184B CYS* 5.6 1.4 - - - -
198B LEU* 3.8 19.3 - - + -
260B LEU 3.1 17.0 + - - +
262B GLU* 3.4 39.4 + - + +
337B ASN* 3.1 20.4 + - - +
338B LEU* 1.4 75.4 - - - +
340B TYR* 1.3 86.2 + - + +
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Residues in contact with TYR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 4.3 9.4 - - + -
149B GLU* 2.6 33.2 + - - +
153B ILE* 3.7 27.6 - - + -
175B ILE* 4.3 3.4 - - + +
176B PHE 3.5 17.9 - - - +
177B LYS* 4.5 10.3 - - + +
178B ILE* 3.8 3.8 - - - -
198B LEU* 4.2 10.8 - - + -
259B LEU* 3.5 0.3 - - - -
260B LEU* 2.9 53.8 + - + -
339B LYS* 1.3 103.3 - - + +
341B LEU* 1.3 62.1 + - - +
342B LEU* 3.4 9.6 + - + +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 34.1 - - + -
140B ILE* 5.1 7.0 - - + -
175B ILE 5.2 0.4 - - - -
176B PHE* 3.1 26.4 + - + +
178B ILE* 3.3 24.8 - - + +
208B PHE* 4.4 11.0 - - + -
212B LEU* 3.8 37.5 - - + -
257B LEU* 4.0 15.7 - - + -
258B ILE 3.8 6.5 - - - +
259B LEU* 4.0 9.0 - - + -
340B TYR* 1.3 72.2 - - - +
342B LEU* 1.3 75.0 + - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ILE* 3.7 16.8 - - + -
154B ARG* 6.0 0.4 - - + -
157B VAL* 3.3 35.0 - - + -
172B VAL* 4.2 14.8 - - + -
174B ASP 3.4 7.6 - - - +
175B ILE* 3.6 28.3 - - + +
200B TRP* 3.6 17.5 - - + -
240B VAL* 5.7 0.4 - - + -
257B LEU* 3.5 1.6 - - - -
258B ILE* 3.0 46.2 + - + +
260B LEU* 4.4 5.8 - - + -
340B TYR* 4.3 9.2 - - + +
341B LEU* 1.3 79.1 - - - +
343B LYS* 1.3 64.8 + - - +
344B LEU* 3.7 5.9 + - + +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO 5.9 0.4 - - - +
10B ASP* 5.1 20.2 + - - +
11B LEU* 4.9 4.9 - - + +
14B MET* 3.6 26.0 - - - -
172B VAL* 4.1 1.6 - - - +
173B ILE* 2.9 40.1 + - + +
174B ASP* 2.9 36.4 + - - +
176B PHE* 3.6 22.1 - - + -
255B ILE* 3.7 24.9 - - + +
256B GLY 3.8 4.9 - - - +
257B LEU* 4.2 12.1 - - + -
341B LEU 3.6 0.8 + - - -
342B LEU* 1.3 69.1 - - - +
344B LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B VAL* 4.8 7.6 - - + -
170B LEU* 3.3 62.8 - - + +
171B GLU 3.4 4.0 - - - +
172B VAL* 4.3 10.5 - - + -
173B ILE* 3.2 15.9 - - - +
240B VAL* 4.5 6.3 - - + -
244B ALA* 4.4 6.5 - - + -
247B CYS* 5.7 0.4 - - - -
255B ILE* 3.3 4.2 - - - +
256B GLY* 3.0 35.6 + - - -
258B ILE* 4.2 27.1 - - + -
342B LEU* 3.7 6.8 + - + -
343B LYS* 1.3 75.2 - - - +
345B LYS* 1.3 63.2 + - - +
346B PHE* 3.3 21.1 - - + -
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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