Contacts of the strand formed by residues 320 - 326 (chain A) in PDB entry 3UAJ
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A MET* 3.8 22.0 - - - -
313A ALA 3.4 4.0 - - - +
314A GLU* 4.0 9.4 - - + -
318A GLY 4.2 0.4 - - - +
319A THR* 1.3 76.2 - - - +
321A VAL* 1.3 61.5 + - - +
367A ILE 3.7 0.9 - - - +
368A GLU* 3.4 2.1 - - - -
369A LEU* 2.7 60.9 + - - +
371A PRO* 3.6 15.8 - - + +
378A ILE* 5.6 0.5 - - - +
391A TRP* 3.5 44.4 - - + +
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Residues in contact with VAL 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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1A MET* 3.8 23.8 - - + -
4A VAL* 3.8 27.1 - - + -
312A MET* 3.4 2.4 - - - -
313A ALA 3.0 29.1 + - - -
315A THR* 3.9 15.9 - - + -
320A THR* 1.3 76.6 - - - +
322A VAL* 1.4 63.6 + - - +
366A ASN* 4.4 2.7 - - - +
367A ILE 3.4 7.4 - - - +
368A GLU* 4.0 18.2 - - + -
101B TRP* 3.2 31.6 - - + -
108B PHE* 4.2 11.0 - - + -
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Residues in contact with VAL 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 ILE* 3.9 22.9 - - + -
310A LYS 3.7 13.9 - - - +
312A MET* 3.8 26.5 - - + +
321A VAL* 1.4 74.7 - - - +
323A LYS* 1.3 65.3 + - - +
324A VAL* 4.6 5.8 - - + -
337A ILE* 5.7 1.6 - - + -
365A THR 3.5 2.8 - - - +
366A ASN* 3.8 1.0 - - - -
367A ILE* 3.0 43.1 + - + +
369A LEU* 3.9 26.9 - - + -
380A ILE* 4.9 12.3 - - + -
389A LEU* 5.1 4.0 - - + -
101B TRP* 3.8 5.6 - - - -
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Residues in contact with LYS 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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308A ILE* 3.5 6.2 - - - +
309A ASP* 2.8 34.6 + - + +
310A LYS* 3.5 40.5 + - + +
322A VAL* 1.3 72.8 - - - +
324A VAL* 1.3 58.2 + - - +
364A VAL* 3.8 24.1 - - + +
365A THR 3.4 3.1 - - - +
366A ASN* 2.8 46.3 + - - +
101B TRP* 3.7 16.3 - - + -
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Residues in contact with VAL 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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306A PHE* 4.0 25.4 - - + -
307A SER 3.4 9.6 - - - +
308A ILE* 3.8 21.5 - - + -
309A ASP* 4.7 0.7 - - - -
322A VAL* 4.6 7.0 - - + -
323A LYS* 1.3 79.5 - - - +
325A LYS* 1.3 58.9 + - - +
326A TYR 4.2 0.2 + - - -
335A VAL* 4.3 9.0 - - + -
337A ILE* 5.2 0.4 - - + -
363A SER 3.5 1.9 - - - +
364A VAL* 3.4 5.3 - - - -
365A THR* 3.0 32.4 + - - +
367A ILE* 3.7 25.8 - - + -
380A ILE* 4.3 24.9 - - + -
387A LEU* 5.3 1.6 - - + -
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Residues in contact with LYS 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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306A PHE* 3.4 9.1 - - - -
307A SER* 2.8 47.5 + - - +
309A ASP* 3.9 23.0 + - + +
324A VAL* 1.3 72.8 - - - +
326A TYR* 1.3 62.9 + - - +
327A GLU* 3.8 5.9 + - + +
362A ASN* 3.6 47.7 - - - +
363A SER 3.4 5.2 - - - +
364A VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 326 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A CYS* 3.6 14.1 - - + -
303A SER* 3.8 6.4 + - - -
304A GLY* 3.5 26.4 + - - -
305A LYS 3.9 3.1 - - - -
306A PHE* 3.4 31.9 - + + -
325A LYS* 1.3 71.6 - - - +
327A GLU* 1.3 64.4 + - - +
328A GLY* 3.5 28.7 - - - -
329A ALA 3.6 1.7 + - - -
330A GLY* 3.1 23.0 + - - -
331A ALA* 3.6 36.3 - - + -
333A CYS* 3.7 9.0 - - - -
358A ALA* 3.9 17.5 - - + -
360A ASN 4.1 10.3 - - - +
361A THR* 4.4 1.1 - - - -
362A ASN* 2.9 32.7 + - - +
363A SER 3.3 11.5 + - - +
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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