Contacts of the strand formed by residues 387 - 391 (chain D) in PDB entry 2UZ1
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 387 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D HIS 3.4 25.4 - - - +
383D VAL* 4.5 3.6 - - + -
384D ASP* 3.0 17.5 + - - +
385D ALA 3.2 1.4 - - - -
386D GLY* 1.3 85.9 - - - +
388D THR* 1.3 75.5 + - - +
389D VAL* 4.0 12.3 - - + -
409D PRO* 3.9 2.1 - - - +
410D GLY* 2.9 25.8 + - - -
411D GLY 3.2 3.3 + - - +
440D ARG* 4.3 2.9 - - - -
441D ARG* 3.2 17.3 - - + +
443D ILE* 3.9 25.4 - - + -
532D LEU* 5.5 4.3 - - + -
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Residues in contact with THR 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 4.8 5.7 - - + +
387D VAL* 1.3 74.8 - - - +
389D VAL* 1.3 66.1 + - - +
390D VAL* 4.1 15.5 - - + -
411D GLY* 3.5 22.5 + - - -
413D LEU* 4.4 9.2 - - + -
431D ALA* 4.4 8.7 - - + -
435D ASP* 2.8 35.2 + - - +
440D ARG* 3.5 10.8 + - - +
441D ARG 2.9 7.7 + - - +
442D THR* 3.4 6.1 - - + +
443D ILE 2.8 28.2 + - - +
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Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ILE* 5.1 3.4 - - + -
383D VAL* 3.8 36.6 - - + -
387D VAL* 4.0 10.3 - - + -
388D THR* 1.3 77.3 - - - +
390D VAL* 1.3 62.9 + - - +
400D LEU* 4.0 19.7 - - + -
404D MET* 4.4 7.6 - - + -
409D PRO* 5.0 0.4 - - + -
411D GLY 2.9 9.7 + - - +
412D PHE* 3.1 31.5 + - + -
413D LEU 2.8 30.5 + - - -
443D ILE* 3.4 8.5 - - + +
445D VAL* 4.2 11.0 - - + -
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Residues in contact with VAL 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D THR* 4.1 8.5 - - + -
389D VAL* 1.3 77.9 - - - +
391D ALA* 1.3 57.9 + - - +
413D LEU* 3.2 27.8 - - + +
424D GLY* 3.8 26.5 - - - +
427D THR* 4.0 16.8 - - + -
428D ALA* 3.8 27.8 - - + -
431D ALA* 4.4 0.4 - - + -
442D THR* 4.0 15.7 - - + -
443D ILE 2.9 8.1 + - - +
444D LEU* 3.4 7.5 - - + +
445D VAL* 2.7 34.3 + - - +
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Residues in contact with ALA 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D VAL* 1.3 78.2 - - - +
392D ASP* 1.3 61.6 + - - +
397D TYR* 3.8 24.2 - - + -
400D LEU* 3.8 22.2 - - + -
412D PHE* 4.2 10.3 - - + -
413D LEU 2.8 11.6 + - - +
414D CYS* 3.7 26.9 - - - -
415D HIS* 3.8 9.5 + - - -
423D VAL* 6.1 0.2 - - - +
424D GLY* 5.2 1.6 - - - -
445D VAL 3.3 4.3 - - - +
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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