Contacts of the strand formed by residues 339 - 346 (chain A) in PDB entry 4Z1H
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 ILE 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A TYR* 3.9 19.3 - - + +
332A LYS* 3.1 7.1 - - - -
333A THR* 2.9 49.1 + - - +
336A PRO* 6.5 0.7 - - + -
337A LEU* 3.7 14.4 - - + +
338A ASN* 1.3 80.7 - - - +
340A ARG* 1.3 68.2 + - - +
341A SER* 3.6 26.0 - - - +
391A VAL* 4.8 5.6 - - + -
392A ASP 3.6 2.5 - - - -
393A SER* 5.0 0.7 - - - -
414A LEU* 3.6 30.3 - - + -
417A VAL* 3.8 23.6 - - + -
418A LEU* 4.4 8.5 - - + -
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Residues in contact with ARG 340 (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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299A TRP* 3.6 20.3 - - + +
300A MET* 3.5 40.2 + - + -
331A TYR 3.7 2.2 - - - -
332A LYS* 3.6 33.1 - - - +
333A THR 4.0 4.2 + - - -
334A ASP* 3.5 24.5 + - - -
338A ASN* 2.4 36.5 + - - +
339A ILE* 1.3 83.2 + - - +
341A SER* 1.3 59.6 + - - +
390A VAL 4.3 0.2 - - - +
391A VAL* 4.0 0.3 - - - -
392A ASP* 2.9 41.4 + - + +
394A GLU* 5.8 0.2 + - - -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 4.6 1.2 + - - +
329A LEU 4.4 0.2 - - - -
330A HIS* 3.4 3.5 - - - -
331A TYR* 2.9 52.6 + - - +
339A ILE* 3.6 13.6 - - - +
340A ARG* 1.3 74.8 - - - +
342A ILE* 1.3 70.0 + - - +
343A PHE* 3.4 24.4 - - - -
390A VAL* 3.2 14.1 - - - -
391A VAL* 3.8 9.4 - - - -
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ILE* 3.8 22.0 - - + +
299A TRP* 3.6 31.4 - - + -
311A HIS* 3.9 21.8 - - + +
314A PHE* 4.5 4.7 - - + -
328A THR* 4.5 1.1 - - + -
329A LEU 3.3 8.3 - - - +
330A HIS* 3.8 12.8 - - + +
341A SER* 1.3 78.7 - - - +
343A PHE* 1.3 68.0 + - - +
344A TYR* 3.3 37.7 - - + +
389A GLY* 3.3 4.5 - - - -
390A VAL* 2.9 39.7 + - + +
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Residues in contact with PHE 343 (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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327A TYR 3.6 0.5 - - - +
328A THR* 3.3 5.9 - - - +
329A LEU* 2.9 59.5 + - + +
331A TYR* 4.7 2.5 - + + -
341A SER* 3.4 19.7 - - - -
342A ILE* 1.3 82.2 - - - +
344A TYR* 1.3 63.7 + - - +
345A VAL* 5.8 0.4 - - - -
363A VAL* 4.5 6.3 - - + -
380A LEU* 4.2 17.5 - - + -
387A ILE* 3.5 28.0 - - + -
388A ARG 3.3 3.6 - - - -
390A VAL 4.4 0.4 - - - -
391A VAL* 3.5 34.3 - - + -
418A LEU* 3.6 24.7 - - + -
421A ARG* 6.0 0.7 - - + -
422A LEU* 4.2 24.0 - - + -
425A PHE* 6.0 0.2 - - - -
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Residues in contact with TYR 344 (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 ILE* 4.1 0.2 - - - +
311A HIS* 3.0 47.0 + - + -
314A PHE* 3.4 33.4 - + - +
315A TYR* 3.5 42.0 - + + -
318A VAL* 4.4 2.5 - - + -
325A PRO* 3.6 11.7 - - + -
327A TYR 3.2 3.4 - - - -
328A THR* 3.2 28.3 - - - -
342A ILE* 3.3 24.3 - - + +
343A PHE* 1.3 77.2 - - - +
345A VAL* 1.3 63.6 + - - +
346A PRO* 3.8 3.1 - - - +
387A ILE* 3.7 7.3 - - - +
388A ARG* 2.8 40.6 + - + +
389A GLY* 4.2 7.2 - - - -
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Residues in contact with VAL 345 (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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325A PRO* 3.2 2.0 - - - -
326A ARG* 2.4 46.8 + - + -
327A TYR* 2.9 32.6 + - + -
343A PHE 5.8 0.7 - - - +
344A TYR* 1.3 70.7 - - - +
346A PRO* 1.3 60.8 - - + +
386A PHE* 4.3 4.3 - - + -
387A ILE* 3.6 28.9 - - + -
425A PHE* 5.5 1.1 - - + -
426A PHE* 3.8 16.2 - - + -
440A PHE* 3.6 22.4 - - + -
444A TYR* 3.8 18.8 - - + -
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Residues in contact with PRO 346 (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* 3.1 33.4 - - + +
323A ASP* 3.7 4.5 - - - +
324A LYS 3.7 3.1 - - - +
326A ARG* 2.7 30.0 + - - -
344A TYR 3.8 7.6 - - - +
345A VAL* 1.3 88.5 - - + +
347A ASP* 1.3 56.0 + - - +
348A MET* 3.4 12.8 - - + +
386A PHE 4.2 13.2 - - - +
388A ARG* 4.4 13.2 - - + +
444A TYR* 3.9 19.9 + - + +
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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