Contacts of the strand formed by residues 387 - 395 (chain A) in PDB entry 4PHZ
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 GLN 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.6 18.4 - - - +
40A MET* 3.8 8.7 - - - +
41A ARG* 3.1 55.4 - - - +
380A LEU* 3.4 9.7 - - - +
385A ASP* 2.8 35.8 + - - +
386A SER* 1.3 74.9 - - - +
388A ILE* 1.3 61.0 + - - +
408A GLY* 3.4 28.5 - - - +
409A PRO* 3.9 11.3 - - - +
410A VAL 4.1 1.8 - - - +
108E ARG* 4.5 3.8 + - - -
266E LYS* 5.6 8.5 - - - +
181F GLN* 5.9 2.1 - - - +
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Residues in contact with ILE 388 (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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40A MET* 3.7 16.6 - - + -
41A ARG* 3.2 12.4 + - - -
288A LEU* 3.7 29.2 - - + -
300A LEU* 4.0 14.6 - - + -
302A ILE* 5.2 5.8 - - + -
319A TYR* 3.7 16.6 - - + +
372A TRP* 3.6 27.8 - - + -
380A LEU* 3.6 22.4 - - + -
387A GLN* 1.3 73.9 - - - +
389A GLY* 1.3 62.5 + - - +
406A ILE* 5.1 4.7 - - + +
407A GLY* 3.2 5.6 - - - +
408A GLY 2.9 29.2 + - - +
410A VAL* 3.8 19.6 - - + +
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Residues in contact with GLY 389 (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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40A MET* 3.6 36.9 - - - +
41A ARG* 4.3 0.9 - - - -
70A PHE* 3.8 10.8 - - - -
319A TYR* 3.0 21.0 + - - -
321A ALA* 4.2 3.3 - - - -
388A ILE* 1.3 77.0 - - - +
390A GLY* 1.3 58.0 + - - -
406A ILE* 3.4 11.7 - - - -
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Residues in contact with GLY 390 (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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40A MET 3.8 0.8 + - - -
44A ASN* 3.8 16.4 - - - -
70A PHE* 3.7 7.3 - - - -
319A TYR* 4.3 0.7 - - - -
320A THR 3.4 11.9 - - - -
321A ALA* 4.8 0.4 - - - -
389A GLY* 1.3 73.9 - - - -
391A LEU* 1.3 63.4 + - - +
405A GLU* 3.4 7.4 - - - +
406A ILE* 2.8 44.3 + - - +
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Residues in contact with LEU 391 (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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44A ASN* 4.0 14.5 - - + +
45A TRP 5.7 0.4 - - - +
46A TYR* 3.8 32.1 - - + -
68A HIS* 3.4 42.2 - - + +
117A ASP* 4.9 1.1 - - - +
277A VAL* 4.1 11.2 - - + -
318A GLU 3.9 0.2 - - - +
319A TYR* 3.4 8.5 - - - -
320A THR* 3.0 36.5 + - + +
390A GLY* 1.3 80.1 - - - +
392A LEU* 1.3 62.5 + - - +
393A PHE* 4.1 28.0 + - + -
403A ALA* 5.1 4.5 - - + -
404A SER 3.4 10.1 - - - +
405A GLU* 4.0 4.3 - - - -
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Residues in contact with LEU 392 (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 THR* 3.8 21.8 - - + +
302A ILE* 5.3 6.7 - - + -
304A VAL* 4.1 16.4 - - + -
316A LEU* 3.8 29.2 - - + -
318A GLU 3.4 0.4 - - - -
319A TYR* 3.7 33.9 - - + -
365A VAL* 5.7 2.2 - - + -
390A GLY 4.1 0.8 + - - -
391A LEU* 1.3 73.4 - - - +
393A PHE* 1.3 61.5 + - - +
394A PHE* 4.0 9.8 - - + -
402A TYR 3.9 0.7 - - - +
403A ALA* 3.3 5.4 - - - +
404A SER* 2.7 48.3 + - - +
406A ILE* 3.8 30.7 - - + -
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Residues in contact with PHE 393 (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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46A TYR* 3.8 37.5 - + + -
316A LEU* 3.5 2.6 - - - +
317A GLY 2.8 25.6 + - - -
318A GLU* 2.7 49.4 + - + -
320A THR* 4.0 17.7 - - - -
391A LEU* 4.1 21.1 - - + -
392A LEU* 1.3 72.2 - - - +
394A PHE* 1.3 63.0 + - - +
395A PHE* 3.4 14.7 - - + -
401A ARG* 3.3 38.6 - - + -
402A TYR 3.9 0.7 - - - -
403A ALA* 3.4 31.2 - - + -
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Residues in contact with PHE 394 (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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284A VAL* 3.6 31.0 - - + -
286A THR* 3.8 17.7 - - + -
306A VAL* 3.9 25.4 - - + -
314A LEU* 4.1 17.5 - - + -
315A ARG 3.3 4.0 - - - +
316A LEU* 3.5 44.9 - - + -
355A ILE* 4.0 25.4 - - + -
363A ILE* 4.7 1.3 - - + -
392A LEU* 4.0 13.9 - - + -
393A PHE* 1.3 75.9 - - - +
395A PHE* 1.3 61.9 + - - +
400A LYS 3.9 0.2 - - - +
401A ARG* 3.3 5.0 - - - -
402A TYR* 2.7 47.8 + - - +
404A SER* 3.9 6.7 - - - -
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Residues in contact with PHE 395 (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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313A PRO 3.9 0.2 - - - +
314A LEU* 3.3 7.3 - - - -
315A ARG* 2.6 46.2 + - - +
317A GLY* 3.6 24.5 - - - -
318A GLU* 4.7 1.8 - - - -
331A VAL* 3.6 20.2 - - + -
332A PHE* 3.5 29.2 - + - -
393A PHE* 3.4 37.9 - - + -
394A PHE* 1.3 71.4 - - - +
396A SER* 1.3 68.1 + - - +
398A ASP 5.2 0.7 - - - +
399A GLY 3.6 19.3 - - - +
400A LYS 3.4 2.9 - - - +
401A ARG* 3.5 31.0 - - + -
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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