Contacts of the strand formed by residues 380 - 383 (chain A) in PDB entry 4ZGY
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 TRP 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS 5.6 1.8 - - - -
28A ILE* 3.5 49.1 + - + +
37A LYS* 3.4 37.9 - - + -
38A ASP 3.6 13.0 - - - -
39A ALA* 4.5 0.2 - - - -
40A PHE* 3.8 17.0 - + - -
287A ALA* 3.8 28.9 - - + -
288A VAL* 3.2 30.1 - - - -
289A ASN* 3.5 17.2 - - + +
340A LEU* 5.2 0.3 - - - -
341A GLN* 4.1 29.6 + - + +
342A LYS* 4.8 8.5 - - - +
375A MET* 4.9 2.6 - - - +
378A GLY 3.8 7.8 + - - -
379A ASP* 1.3 78.9 - - - +
381A MET* 1.3 69.6 + - - +
382A LEU* 5.3 2.2 - - + -
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Residues in contact with MET 381 (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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286A LEU 3.6 0.9 - - - +
287A ALA* 3.5 2.6 - - - -
288A VAL* 2.9 43.5 + - + +
290A ILE* 3.7 20.4 - - + -
316A TYR* 4.8 2.9 - - + -
318A VAL* 3.6 29.6 - - + -
338A PRO* 4.1 11.0 - - + -
339A LEU 3.8 10.8 - - - +
340A LEU* 5.1 2.5 - - + -
355A ILE* 3.6 35.4 - - + -
372A LEU* 4.4 3.1 - - + -
375A MET* 3.7 28.3 - - + -
380A TRP* 1.3 79.2 - - - +
382A LEU* 1.3 66.1 + - - +
383A PHE* 4.2 7.5 - - + -
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Residues in contact with LEU 382 (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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21A LYS* 4.1 22.9 - - + +
24A LEU* 3.9 26.0 - - + -
28A ILE* 5.6 0.9 - - + -
285A THR* 4.3 9.4 - - + -
286A LEU 3.3 3.4 - - - +
287A ALA* 3.6 30.3 - - + -
338A PRO 3.6 0.7 - - - -
339A LEU* 2.7 52.4 + - + +
340A LEU 4.7 0.9 - - - +
341A GLN* 3.8 41.5 - - + +
380A TRP* 5.3 2.0 - - + -
381A MET* 1.3 77.8 - - - +
383A PHE* 1.3 65.5 + - - +
384A GLU* 4.2 0.4 - - + -
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Residues in contact with PHE 383 (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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285A THR* 3.5 1.4 - - - -
286A LEU* 2.9 43.0 + - + +
288A VAL* 3.9 28.7 - - + -
318A VAL* 5.9 0.9 - - + -
326A PHE* 4.0 21.3 - + + -
336A VAL* 4.0 29.2 - - + -
337A LYS 3.7 17.0 - - - -
338A PRO* 3.7 29.4 - - + -
355A ILE* 4.3 16.4 - - + -
366A ILE* 4.5 7.4 - - + -
367A VAL* 4.3 4.7 - - + -
381A MET* 4.2 13.9 - - + -
382A LEU* 1.3 75.2 - - - +
384A GLU* 1.3 63.1 + - - +
386A MET* 3.3 23.6 - - + +
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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