Contacts of the strand formed by residues 304 - 312 (chain A) in PDB entry 1UCU
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 ALA 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU* 4.0 18.1 - - + +
292A LYS* 4.3 20.7 + - + +
295A LEU* 3.5 31.9 - - + -
302A GLY 3.8 2.4 + - - +
303A THR* 1.3 83.6 - - - +
305A SER* 1.3 64.5 + - - +
325A VAL* 3.7 11.2 - - + -
326A LYS 3.3 5.8 - - - -
327A VAL* 4.3 0.9 - - - -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.2 5.6 - - - +
303A THR 5.1 0.9 + - - -
304A ALA* 1.3 77.8 - - - +
306A VAL* 1.3 65.5 - - - +
307A VAL* 4.2 6.5 - - - +
325A VAL* 3.3 4.3 - - - -
326A LYS* 2.8 49.7 + - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA* 3.9 2.9 - - - +
185A ALA 3.0 35.9 + - - +
187A VAL* 4.2 10.8 - - + +
288A LEU* 3.4 34.1 - - + +
305A SER* 1.3 74.4 - - - +
307A VAL* 1.3 65.5 + - - +
323A LEU* 3.8 26.2 - - + -
324A ALA 3.3 9.6 - - - +
342A ILE* 3.4 27.8 - - + -
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Residues in contact with VAL 307 (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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182A ASP* 3.4 39.5 - - + +
183A THR 3.3 11.9 - - - +
184A ALA* 4.2 7.0 - - + -
185A ALA* 4.0 5.4 - - - +
305A SER* 4.2 8.7 - - - +
306A VAL* 1.3 78.4 - - - +
308A LYS* 1.3 59.5 + - - +
309A MET* 4.1 4.7 - - - -
323A LEU* 3.4 9.2 - - - +
324A ALA* 2.8 51.9 + - + +
326A LYS* 4.1 25.8 - - + -
331A TYR* 4.2 1.3 - - + -
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Residues in contact with LYS 308 (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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182A ASP* 3.2 6.0 - - - -
183A THR* 2.8 48.5 + - - +
184A ALA 5.5 0.4 - - - +
185A ALA* 4.5 10.3 - - + -
307A VAL* 1.3 73.2 - - - +
309A MET* 1.3 83.7 + - - +
310A SER* 3.7 11.0 + - - -
320A ASP* 2.9 37.7 + - + -
321A GLY 4.6 3.8 - - - +
322A GLY 3.7 9.6 - - - +
323A LEU* 4.7 5.6 - - + -
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Residues in contact with MET 309 (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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180A VAL* 3.4 27.4 - - + -
181A SER 3.3 21.1 - - - +
182A ASP* 4.4 0.2 - - - -
307A VAL* 4.1 4.9 - - - -
308A LYS* 1.3 81.6 - - - +
310A SER* 1.3 60.2 + - - +
311A TYR* 3.5 31.4 - - + +
320A ASP* 3.6 0.5 - - - -
321A GLY* 2.7 27.5 + - - -
322A GLY 3.0 20.4 + - - +
323A LEU 4.8 0.2 - - - -
324A ALA* 3.6 21.8 - - + -
331A TYR* 3.4 37.9 - - + -
363A LEU* 3.9 8.3 - - + -
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Residues in contact with SER 310 (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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181A SER* 3.0 47.8 + - - +
182A ASP* 5.0 1.7 - - - -
183A THR* 5.0 4.3 + - - +
308A LYS* 3.7 21.1 + - - -
309A MET* 1.3 79.0 + - - +
311A TYR* 1.3 71.4 + - - +
312A THR* 5.8 0.4 - - - -
318A THR* 5.0 9.2 - - - -
319A ILE 3.4 11.2 - - - -
320A ASP* 4.1 3.0 + - - -
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Residues in contact with TYR 311 (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 TYR* 3.8 25.1 - - + -
179A LYS 3.5 3.8 - - - -
180A VAL* 4.0 26.0 - - + -
309A MET* 3.5 16.4 - - + +
310A SER* 1.3 80.9 - - - +
312A THR* 1.3 62.2 + - - +
313A ASP 4.2 0.2 + - - -
317A LYS 3.7 1.6 - - - +
318A THR* 3.1 2.5 - - - -
319A ILE* 3.0 48.3 + - + +
321A GLY* 3.6 29.5 - - - -
322A GLY 5.2 0.9 + - - -
363A LEU* 3.4 29.0 - - + +
368A GLY 4.0 9.6 - - - -
369A LYS* 3.3 44.4 - - + +
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Residues in contact with THR 312 (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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105A GLN* 4.3 0.2 - - - +
178A TYR* 3.6 5.1 - - - -
179A LYS* 2.8 56.8 + - + +
181A SER* 5.2 4.3 + - - -
310A SER* 5.4 0.7 - - - -
311A TYR* 1.3 72.2 + - - +
313A ASP* 1.3 74.7 + - - +
316A GLY* 3.8 25.4 - - - +
317A LYS 3.3 3.4 - - - +
318A THR* 3.0 22.9 - - + +
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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