Contacts of the strand formed by residues 403 - 408 (chain A) in PDB entry 2ZDZ
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 PHE 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU 3.9 6.4 - - - +
215A GLN* 4.4 5.5 - - - -
216A LEU 4.5 1.6 + - - +
360A ILE* 3.7 24.7 - - + -
361A THR 3.4 21.5 - - - -
362A ILE* 3.5 19.1 - - + -
399A ILE* 3.0 31.2 - - + -
400A MET* 2.9 16.7 + - - +
401A GLU 3.3 0.8 - - - -
402A GLY* 1.3 89.7 - - - +
404A TYR* 1.3 60.7 + - - +
405A VAL* 3.9 6.1 + - + +
416A PHE* 4.2 27.6 - + + -
417A ALA 3.3 9.4 - - - +
418A VAL* 4.4 1.6 - - - -
419A SER* 3.6 11.0 + - - -
430A ALA* 4.2 4.0 - - + -
431A ALA 3.4 26.7 - - - -
432A VAL* 3.5 20.6 - - + -
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Residues in contact with TYR 404 (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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213A SER* 2.5 35.3 + - - -
214A LEU 3.7 15.3 - - - -
215A GLN* 3.8 16.2 - - + +
237A ILE* 3.7 6.5 - - + +
241A ILE* 3.7 13.7 - - + -
242A ASP* 3.0 34.8 + - - +
245A LEU* 3.7 31.9 - - + +
246A TYR* 3.4 43.1 - + + -
250A LEU* 4.2 5.2 - - + +
403A PHE* 1.3 70.7 - - - +
405A VAL* 1.3 60.1 + - - +
406A VAL* 4.0 11.1 + - + -
415A GLY 3.5 5.0 - - - +
416A PHE* 3.6 1.6 - - - -
417A ALA* 2.7 30.3 + - + +
419A SER* 3.9 3.2 - - - -
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Residues in contact with VAL 405 (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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213A SER* 3.3 2.5 - - - -
214A LEU 2.8 39.1 + - - +
289A VAL* 4.4 4.3 - - + -
400A MET* 4.3 24.7 - - + +
403A PHE* 4.1 14.4 - - + +
404A TYR* 1.3 76.0 - - - +
406A VAL* 1.3 64.1 + - - +
407A PHE* 3.5 30.4 - - + -
414A ILE* 3.7 23.3 - - + -
415A GLY 3.3 4.0 - - - +
416A PHE* 3.9 26.7 - - + -
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Residues in contact with VAL 406 (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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211A LEU* 3.9 33.7 - - + -
212A PHE 3.9 2.7 - - - +
213A SER* 4.1 9.0 - - - -
241A ILE* 3.9 28.7 - - + -
250A LEU* 3.8 26.5 - - + -
252A TYR* 4.5 4.9 - - + -
404A TYR* 4.3 8.7 - - + -
405A VAL* 1.3 72.6 - - - +
407A PHE* 1.3 62.5 + - - +
408A ASP* 3.3 10.1 + - + +
414A ILE* 3.2 10.1 - - - +
415A GLY* 2.8 42.6 + - - +
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Residues in contact with PHE 407 (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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95A THR* 3.8 23.1 - - + -
211A LEU* 3.5 1.6 - - - -
212A PHE* 2.7 64.2 + + + +
213A SER* 4.8 0.2 - - - -
214A LEU* 3.7 19.1 - - + -
255A ILE* 5.6 0.2 - - - -
261A TYR* 3.7 44.0 - + + -
289A VAL* 3.7 31.2 - - + -
400A MET* 3.9 6.3 - - + -
405A VAL* 3.5 29.8 - - + -
406A VAL* 1.3 71.0 - - - +
408A ASP* 1.3 58.3 + - - +
409A ARG* 3.0 13.5 + - - +
413A ARG 4.3 1.8 - - - -
414A ILE* 4.5 9.6 - - + -
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Residues in contact with ASP 408 (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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211A LEU* 3.5 29.6 - - + +
252A TYR* 4.3 5.7 + - + -
255A ILE* 4.8 0.9 - - - -
406A VAL* 3.3 8.2 + - + -
407A PHE* 1.3 69.0 - - - +
409A ARG* 1.3 56.2 + - - +
410A ALA* 3.6 8.8 + - - +
411A ARG* 3.2 23.8 + - - +
412A LYS* 3.0 22.3 + - - -
413A ARG* 2.9 64.5 + - + +
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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