Contacts of the strand formed by residues 318 - 327 (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 THR 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A SER* 5.0 7.7 - - - -
311A TYR 3.1 8.5 - - - -
312A THR* 3.0 27.8 - - + +
316A GLY 3.7 11.7 - - - +
317A LYS* 1.3 82.3 - - - +
319A ILE* 1.3 67.9 + - - +
320A ASP* 5.1 3.5 + - - -
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Residues in contact with ILE 319 (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* 5.2 8.7 - - + +
310A SER* 3.4 4.0 - - - -
311A TYR* 3.0 51.3 + - + +
317A LYS* 4.3 22.2 - - + +
318A THR* 1.3 79.6 - - - +
320A ASP* 1.3 71.5 + - - +
369A LYS* 4.6 16.8 - - + -
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Residues in contact with ASP 320 (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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308A LYS* 2.9 36.0 + - + -
309A MET 3.6 3.8 - - - -
310A SER* 4.1 4.4 + - - +
311A TYR* 4.7 0.2 - - - -
318A THR* 5.1 4.0 + - - +
319A ILE* 1.3 89.1 - - - +
321A GLY* 1.3 65.9 + - - +
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Residues in contact with GLY 321 (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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308A LYS* 4.6 5.2 - - - +
309A MET* 2.7 18.6 + - - +
311A TYR* 3.6 23.8 - - - -
319A ILE* 3.9 0.4 + - - -
320A ASP* 1.3 80.9 - - - +
322A GLY* 1.3 64.7 - - - +
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Residues in contact with GLY 322 (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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308A LYS* 3.7 4.7 - - - -
309A MET* 3.0 31.9 + - - +
311A TYR* 5.0 1.0 + - - -
321A GLY* 1.3 74.5 - - - -
323A LEU* 1.3 66.5 + - - -
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Residues in contact with LEU 323 (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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185A ALA* 3.8 23.1 - - + -
187A VAL* 4.6 7.9 - - + -
306A VAL* 3.8 14.6 - - + -
307A VAL 3.4 15.5 - - - +
308A LYS* 4.7 7.0 - - + -
309A MET* 5.0 0.5 - - - +
322A GLY* 1.3 75.8 - - - -
324A ALA* 1.3 62.4 + - - +
333A SER* 4.0 3.3 - - - -
334A ALA* 3.1 38.8 + - + +
335A THR* 5.1 0.7 - - - -
336A GLN* 3.9 39.9 - - + +
342A ILE* 5.8 3.4 - - + -
363A LEU* 5.5 0.5 - - - +
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Residues in contact with ALA 324 (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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305A SER 3.5 0.2 - - - +
306A VAL* 3.3 7.5 - - - +
307A VAL* 2.8 36.9 + - + -
309A MET* 3.6 33.2 - - + -
323A LEU* 1.3 76.8 - - - +
325A VAL* 1.3 64.3 + - - +
326A LYS 3.7 0.7 - - - -
331A TYR* 4.4 6.5 - - + -
332A TYR 3.4 15.7 - - - +
334A ALA* 4.0 2.7 - - - +
363A LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 325 (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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288A LEU* 4.9 3.6 - - + -
291A ALA* 4.5 5.6 - - + -
295A LEU* 3.7 17.3 - - + -
304A ALA* 3.7 29.6 - - + -
305A SER 3.3 7.0 - - - +
306A VAL* 5.1 0.7 - - + -
324A ALA* 1.3 71.3 - - - +
326A LYS* 1.3 58.0 + - - +
327A VAL* 4.0 1.1 - - + -
332A TYR* 2.9 42.1 + - + +
334A ALA* 3.7 11.0 - - + -
342A ILE* 3.4 33.0 - - + -
344A ILE* 3.9 23.6 - - + -
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Residues in contact with LYS 326 (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* 2.9 36.3 + - - +
303A THR 3.5 2.4 - - - +
304A ALA* 3.3 2.8 - - - -
305A SER* 2.8 44.0 + - - +
307A VAL* 4.1 16.6 - - + -
324A ALA 3.7 2.0 - - - -
325A VAL* 1.3 72.0 - - - +
327A VAL* 1.3 66.6 + - - +
328A GLY 3.8 19.3 - - - +
329A ASP* 5.1 5.6 - - - +
330A ASP 3.6 11.4 - - - +
331A TYR* 3.8 20.9 + - + -
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Residues in contact with VAL 327 (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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295A LEU* 3.4 30.5 - - + -
300A VAL* 3.2 27.0 - - + +
302A GLY* 3.8 31.0 - - - +
303A THR 3.8 4.3 - - - +
304A ALA* 4.2 2.0 - - + -
325A VAL* 3.9 3.8 - - + +
326A LYS* 1.3 79.7 - - - +
328A GLY* 1.3 65.9 + - - +
329A ASP 3.2 0.2 + - - -
330A ASP* 3.0 27.4 + - - +
332A TYR* 3.6 26.2 - - + -
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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