Contacts of the strand formed by residues 327 - 331 (chain A) in PDB entry 4Z7Q
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 ARG 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLU* 2.8 26.3 + - - -
308A VAL 4.0 0.2 - - - +
309A GLY* 3.7 0.3 - - - -
310A ALA* 2.8 33.0 + - - +
313A TYR* 3.1 49.1 + - + -
315A GLU* 4.7 9.7 + - - +
326A GLY* 1.3 76.0 - - - +
328A VAL* 1.3 78.4 + - - +
329A TYR* 3.4 31.9 - - + -
346A LEU* 3.8 24.5 - - - +
347A LEU 3.2 13.0 - - - +
348A THR* 2.9 26.7 + - - +
356A PHE* 3.1 5.2 + - - +
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Residues in contact with VAL 328 (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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307A LEU* 4.0 22.9 - - + -
308A VAL 3.4 9.4 - - - +
327A ARG* 1.3 79.9 - - - +
329A TYR* 1.3 67.1 + - - +
345A LEU 3.8 0.3 - - - +
346A LEU* 3.6 5.5 - - - -
347A LEU* 2.6 49.5 + - + +
356A PHE* 3.5 22.4 - - + -
357A GLY* 3.7 20.2 - - - -
360A ILE* 3.8 19.1 - - + -
376A VAL* 3.8 16.4 - - + -
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Residues in contact with TYR 329 (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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283A GLU* 2.7 47.8 + - + +
284A GLN 5.1 0.2 + - - -
287A SER* 5.5 0.9 + - - -
289A PHE* 3.6 34.5 - + + +
306A LEU 3.6 1.2 - - - +
307A LEU* 3.3 7.8 - - - +
308A VAL* 2.9 40.0 + - + +
310A ALA* 3.9 15.1 - - + +
313A TYR* 3.8 10.7 - - - -
327A ARG* 3.4 22.7 - - + -
328A VAL* 1.3 77.1 - - - +
330A LEU* 1.3 59.2 + - - +
331A PHE* 3.5 22.6 - + + -
343A PRO* 3.9 13.5 - - + -
345A LEU 3.8 2.9 - - - -
346A LEU* 3.2 28.3 - - + -
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Residues in contact with LEU 330 (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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298A VAL* 4.2 16.4 - - + -
305A ASP* 4.4 7.0 - - + -
306A LEU 3.6 5.4 - - - +
307A LEU* 3.8 26.2 - - + -
328A VAL 4.2 0.2 + - - -
329A TYR* 1.3 72.5 - - - +
331A PHE* 1.3 61.3 - - - +
332A LEU* 4.2 17.5 - - + -
343A PRO* 3.3 4.2 - - - +
344A SER* 2.7 36.2 + - - -
345A LEU* 3.1 34.8 + - + +
347A LEU* 6.5 0.4 - - + -
398A GLY* 4.1 10.5 - - - -
399A LEU* 4.0 38.4 - - + +
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Residues in contact with PHE 331 (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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280A LEU* 3.7 33.4 - - + -
281A ARG 5.9 0.7 - - - -
289A PHE* 4.5 7.9 - + - -
305A ASP* 3.6 4.1 - - - -
306A LEU* 2.8 55.3 + - + +
308A VAL* 4.1 20.9 - - + -
329A TYR* 3.5 26.0 - + + -
330A LEU* 1.3 73.1 - - - +
332A LEU* 1.3 65.0 + - - +
333A GLN 3.7 0.7 + - - -
340A LEU* 4.1 22.0 - - + +
341A GLY 3.7 18.4 - - - -
342A ALA 4.2 1.8 - - - -
343A PRO* 3.6 39.9 - - + -
344A SER* 4.5 1.3 - - - +
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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