Contacts of the strand formed by residues 330 - 336 (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 ASP 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A LYS* 3.6 4.9 - - - +
327A VAL 3.0 35.5 + - - +
329A ASP* 1.3 86.2 + - - +
331A TYR* 1.3 62.0 + - - +
332A TYR* 3.9 12.5 + - + +
362A LYS* 3.0 39.4 + - + +
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Residues in contact with TYR 331 (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* 3.8 23.3 + - + +
181A SER* 4.3 10.4 - - - -
182A ASP* 2.8 33.3 + - + +
307A VAL* 4.2 6.1 - - + -
309A MET* 3.4 31.2 - - + -
324A ALA* 4.4 2.7 - - + -
325A VAL 3.8 2.5 - - - -
326A LYS* 3.8 30.5 + - + -
329A ASP 3.7 16.4 - - - -
330A ASP* 1.3 73.3 - - - +
332A TYR* 1.3 62.5 + - - +
333A SER 4.0 0.2 - - - -
362A LYS* 3.0 10.4 - - - +
363A LEU* 2.8 54.5 + - + +
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Residues in contact with TYR 332 (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* 4.0 11.0 - - + -
300A VAL* 3.2 33.0 - - + +
324A ALA* 3.4 2.1 - - - -
325A VAL* 2.9 46.6 + - + +
327A VAL* 3.6 28.5 - - + -
330A ASP* 3.9 18.1 + - + +
331A TYR* 1.3 73.2 - - - +
333A SER* 1.3 67.0 + - - +
334A ALA* 3.1 2.1 + - - +
344A ILE* 3.7 21.3 - - + -
360A LEU* 4.1 25.1 - - + -
361A ASN 3.2 15.3 - - - +
362A LYS* 3.1 33.1 + - + -
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Residues in contact with SER 333 (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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323A LEU 4.0 7.4 - - - -
331A TYR 4.0 1.6 - - - -
332A TYR* 1.3 72.1 - - - +
334A ALA* 1.3 60.4 + - - +
344A ILE* 3.7 3.5 - - - +
345A ASN* 2.9 29.7 + - - -
361A ASN* 3.0 22.6 + - - +
363A LEU* 3.9 27.5 - - - +
371A GLU* 2.7 30.8 + - - +
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Residues in contact with ALA 334 (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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323A LEU* 3.1 31.5 + - + +
324A ALA* 4.2 3.8 - - - -
325A VAL* 3.7 29.4 - - + -
332A TYR 3.8 1.6 - - - +
333A SER* 1.3 75.9 - - - +
335A THR* 1.3 66.5 + - - +
342A ILE* 3.8 13.7 - - + -
343A SER 3.3 13.0 - - - +
344A ILE* 4.3 0.2 - - - -
345A ASN* 3.7 4.9 + - - +
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Residues in contact with THR 335 (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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323A LEU* 5.1 3.1 - - - -
334A ALA* 1.3 75.9 + - - +
336A GLN* 1.3 73.4 + - - +
337A ASN* 3.9 9.0 - - - +
342A ILE* 3.2 5.7 - - - +
343A SER* 2.8 39.0 + - - -
345A ASN* 2.9 21.9 + - - -
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Residues in contact with GLN 336 (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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187A VAL* 3.2 33.5 - - + +
323A LEU* 3.9 23.2 - - + +
335A THR* 1.3 80.1 - - - +
337A ASN* 1.3 73.9 + - - +
338A LYS 5.7 0.4 + - - -
340A GLY* 3.8 15.8 - - - +
341A SER 3.2 14.4 - - - +
342A ILE* 4.2 5.4 - - + +
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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