Contacts of the strand formed by residues 384 - 389 (chain A) in PDB entry 4X2Q
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 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A PHE* 3.7 5.1 - - - -
357A ILE* 4.6 5.2 - - + +
367A LEU* 3.9 6.1 - - + -
369A CYS 3.2 17.0 - - - +
371A GLY* 2.9 28.8 + - - +
381A ILE* 4.7 0.7 - - - +
382A GLU 3.0 11.3 + - - -
383A PRO* 1.3 71.7 - - - +
385A VAL* 1.3 67.6 + - - +
386A PHE* 3.7 30.5 - - + -
403A PRO 3.2 13.0 + - - -
404A VAL* 3.6 14.5 - - + +
405A GLN 3.3 22.7 + - - -
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Residues in contact with VAL 385 (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 PHE* 4.9 1.6 - - + -
319A VAL* 5.5 1.1 - - + -
322A SER* 4.3 15.0 - - - +
323A VAL* 4.5 8.3 - - + -
326A ALA* 4.3 13.7 - - + -
366A LYS 3.8 0.2 - - - +
367A LEU 4.1 0.3 - - - -
368A GLU* 3.1 40.9 + - + +
369A CYS* 3.6 24.6 + - - +
384A THR* 1.3 82.0 - - - +
386A PHE* 1.3 68.9 + - - +
387A SER* 5.7 0.2 - - - -
405A GLN* 3.7 22.2 - - + +
407A ILE* 3.8 29.2 - - + -
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Residues in contact with PHE 386 (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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356A LEU 5.5 0.4 - - - -
357A ILE* 3.5 35.4 - - + -
360A GLY* 4.6 2.7 - - - -
361A VAL* 3.9 15.7 - - + -
365A ALA* 3.7 28.0 - - + -
366A LYS 3.5 14.4 - - - -
367A LEU* 3.7 35.0 - - + -
384A THR* 3.7 15.7 - - + -
385A VAL* 1.3 75.0 - - - +
387A SER* 1.3 60.6 + - - +
389A VAL* 3.9 8.8 - - + +
395A ILE* 5.0 10.8 - - + -
404A VAL* 3.7 26.5 - - + -
405A GLN 3.1 11.3 + - - +
406A GLU* 3.7 5.3 - - + -
407A ILE* 2.9 31.4 + - - +
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Residues in contact with SER 387 (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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315A TYR* 3.3 12.4 + - - -
319A VAL* 4.2 13.2 - - - +
365A ALA* 3.5 4.2 - - - +
366A LYS* 3.1 33.5 + - - -
368A GLU* 3.9 29.1 - - - +
385A VAL* 5.9 0.7 - - - -
386A PHE* 1.3 74.2 - - - +
388A ASN* 1.3 89.6 + - - +
389A VAL 3.6 1.6 - - - -
407A ILE* 4.1 5.2 - - - -
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Residues in contact with ASN 388 (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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315A TYR* 2.9 25.8 + - - -
364A GLY 4.6 5.8 - - - +
365A ALA* 4.1 11.1 + - - -
366A LYS* 5.1 7.4 - - + +
387A SER* 1.3 100.8 + - - +
389A VAL* 1.3 60.0 + - - +
390A THR* 4.1 4.3 + - - +
393A MET* 4.7 2.3 - - - +
407A ILE 3.6 0.6 + - - -
409A ARG* 5.1 11.5 + - - +
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Residues in contact with VAL 389 (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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365A ALA* 4.1 13.2 - - + -
386A PHE* 3.9 17.3 - - + +
387A SER 4.0 4.9 - - - +
388A ASN* 1.3 77.5 - - - +
390A THR* 1.3 75.6 + - - +
393A MET* 3.8 14.1 - - - -
395A ILE* 3.9 15.9 - - + -
396A ALA* 4.5 5.2 - - + -
406A GLU* 3.8 29.2 - - + -
407A ILE 3.7 7.0 + - - +
408A LEU* 3.3 39.2 - - + +
409A ARG 4.6 2.9 + - - -
419A ARG* 5.0 1.9 + - - -
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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