Contacts of the strand formed by residues 359 - 364 (chain F) in PDB entry 2HU4
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 GLY 359 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355F LYS* 3.7 1.7 - - - +
356F TYR 2.8 28.6 + - - -
358F ASN* 1.3 80.8 - - - +
360F VAL* 1.3 72.2 + - - +
378F TRP* 3.8 8.5 - - - -
379F ASP 3.2 13.5 - - - -
380F PRO* 3.8 5.2 - - - -
381F ASN 3.3 9.9 - - - +
383F TRP* 4.0 1.2 - - - +
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Residues in contact with VAL 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F ILE* 4.7 4.7 - - + -
353F SER* 5.2 3.8 - - - -
354F PHE 3.2 11.7 - - - +
355F LYS* 4.2 0.2 - - - -
359F GLY* 1.3 82.9 - - - +
361F TRP* 1.3 60.1 + - - +
362F ILE* 3.8 27.6 - - + -
377F ILE 3.5 2.1 - - - +
378F TRP* 3.1 12.2 - - - -
379F ASP* 2.9 36.1 + - + +
382F GLY* 3.7 23.1 - - - +
383F TRP* 3.0 44.2 - - + -
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Residues in contact with TRP 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F ILE* 3.7 29.5 + - + +
95F ASN* 3.7 30.3 - - - -
96F GLY* 4.4 1.6 - - - -
97F TRP* 3.1 46.2 - + + -
353F SER* 3.2 9.0 - - - -
354F PHE* 2.8 39.8 + - + +
356F TYR* 4.0 15.0 - + - -
360F VAL* 1.3 73.0 - - - +
362F ILE* 1.3 59.0 + - - +
376F MET* 3.7 33.3 - - + +
377F ILE 3.5 16.4 - - - -
378F TRP* 3.7 46.6 - + + -
392F VAL* 4.6 13.2 - - + -
395F GLN* 4.8 2.7 - - + -
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Residues in contact with ILE 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F ARG* 6.4 0.4 - - - -
317F ILE* 4.6 9.4 - - + -
319F SER* 4.2 15.9 - - - +
321F VAL* 3.9 25.8 - - + +
323F GLY* 4.2 18.4 - - - +
353F SER* 3.9 15.7 - - - +
360F VAL* 3.8 27.4 - - + -
361F TRP* 1.3 78.0 - - - +
363F GLY* 1.3 74.3 + - - +
364F ARG* 4.5 8.4 - - + +
375F GLU 3.5 5.0 - - - +
376F MET* 3.5 6.7 - - - -
377F ILE* 2.8 43.3 + - + +
379F ASP* 4.8 5.4 - - + -
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Residues in contact with GLY 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F ARG* 4.8 5.2 + - - -
323F GLY* 3.8 7.3 - - - +
351F GLY* 5.5 0.7 - - - -
352F PHE* 3.6 26.7 + - - +
361F TRP 4.2 0.4 + - - -
362F ILE* 1.3 80.3 - - - +
364F ARG* 1.3 65.8 + - - +
374F PHE* 3.7 16.8 - - - -
375F GLU 3.7 5.8 - - - -
376F MET* 3.9 9.9 - - - +
407F SER* 5.1 1.6 - - - -
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Residues in contact with ARG 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F VAL* 2.9 21.1 - - - +
322F PHE 2.9 25.4 + - - -
323F GLY* 3.6 18.8 - - - +
327F ARG* 3.3 23.1 - - - +
330F ASP* 2.7 42.8 + - - -
362F ILE* 4.5 5.6 - - + +
363F GLY* 1.3 77.1 - - - +
365F THR* 1.3 70.5 + - - +
374F PHE* 3.3 18.1 - - - -
375F GLU* 3.1 52.3 + - + +
377F ILE* 3.5 21.6 - - + +
390F PHE* 5.3 2.0 - - - -
394F LYS* 4.5 4.2 - - - +
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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