Contacts of the strand formed by residues 364 - 370 (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 VAL 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASN 5.0 2.1 - - - +
309A ASP* 3.5 36.1 - - + +
323A LYS* 3.8 44.4 - - + +
324A VAL 3.4 4.5 - - - +
325A LYS* 4.0 17.0 - - + -
362A ASN 4.7 0.9 - - - +
363A SER* 1.3 80.0 + - - +
365A THR* 1.4 64.6 + - - +
366A ASN* 4.5 1.8 + - - +
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Residues in contact with THR 365 (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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145A ASN* 4.4 9.2 - - - +
306A PHE* 5.8 0.6 - - - -
323A LYS* 3.4 5.2 - - - -
324A VAL* 3.0 33.4 + - - -
335A VAL* 4.6 6.9 - - + +
356A PRO* 4.1 17.3 - - + -
357A LEU 3.0 31.9 + - - +
358A ALA* 3.9 10.0 - - - +
359A GLU 5.1 0.2 + - - -
363A SER* 4.4 4.3 + - - -
364A VAL* 1.4 76.3 + - - +
366A ASN* 1.3 66.4 + - - +
367A ILE* 3.4 24.6 - - + +
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Residues in contact with ASN 366 (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 32.1 - - + +
145A ASN* 3.3 33.4 + - - +
321A VAL* 4.4 0.8 - - - +
322A VAL 3.8 2.9 - - - -
323A LYS* 2.8 47.6 + - - +
353A SER* 4.2 9.0 + - - -
356A PRO* 5.0 1.4 - - - +
364A VAL* 5.0 1.7 - - - +
365A THR* 1.3 75.5 - - - +
367A ILE* 1.3 63.3 + - - +
101B TRP* 4.0 13.3 - - - -
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Residues in contact with ILE 367 (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* 5.4 1.1 - - - -
320A THR 3.7 1.7 - - - +
321A VAL* 3.4 7.4 - - - +
322A VAL* 3.0 42.6 + - + +
324A VAL* 3.7 22.4 - - + -
335A VAL* 5.1 2.2 - - + -
337A ILE* 3.8 21.3 - - + -
351A ILE* 3.8 26.5 - - + -
353A SER* 4.0 3.8 - - - -
356A PRO* 3.7 24.9 - - + -
365A THR* 3.4 34.8 - - + +
366A ASN* 1.3 76.8 - - - +
368A GLU* 1.3 60.8 + - - +
369A LEU* 3.8 16.9 + - + -
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Residues in contact with GLU 368 (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* 5.0 3.1 - - - -
4A VAL* 3.7 10.3 - - - +
9A ARG* 2.8 45.9 + - - -
11A PHE* 4.4 1.7 - - - -
144A HIS* 3.3 15.4 - - + +
315A THR* 4.6 1.2 - - - +
319A THR* 3.0 21.0 + - - +
320A THR 3.4 4.0 - - - +
321A VAL* 4.0 17.7 - - + +
351A ILE* 3.7 4.3 - - - +
352A ILE* 2.8 53.7 + - + +
353A SER* 3.2 21.4 + - - +
367A ILE* 1.3 71.6 - - - +
369A LEU* 1.3 57.3 + - - +
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Residues in contact with LEU 369 (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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312A MET* 3.9 18.8 - - - -
319A THR* 3.4 5.7 - - - -
320A THR* 2.7 50.1 + - - +
322A VAL* 3.9 27.8 - - + -
337A ILE* 3.7 26.9 - - + -
339A ILE* 3.8 14.1 - - + -
350A ARG 4.0 2.7 - - - -
351A ILE* 3.8 21.5 - - + -
352A ILE* 3.5 4.5 - - - -
367A ILE* 3.8 16.2 - - + +
368A GLU* 1.3 74.4 - - - +
370A GLU* 1.3 58.0 + - - +
371A PRO* 3.4 2.4 - - + +
378A ILE* 3.9 18.4 - - + -
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Residues in contact with GLU 370 (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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11A PHE* 6.1 1.4 - - - -
319A THR* 4.3 17.5 - - + +
339A ILE* 4.3 2.2 - - - -
349A GLY* 3.8 4.5 - - - -
350A ARG* 2.8 80.7 + - + +
352A ILE* 3.7 12.1 - - + +
369A LEU* 1.3 72.5 - - - +
371A PRO* 1.4 64.7 - - - +
393A ARG* 4.2 18.5 + - - +
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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