Contacts of the strand formed by residues 359 - 364 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A LYS* 3.4 2.6 - - - +
356A TYR 2.8 30.9 + - - -
358A ASN* 1.3 80.2 - - - +
360A VAL* 1.3 71.9 + - - +
378A TRP* 3.8 13.9 - - - -
379A ASP 3.5 3.6 - - - -
381A ASN 3.3 16.3 - - - +
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Residues in contact with VAL 360 (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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317A ILE* 4.6 6.5 - - + -
353A SER* 5.1 3.8 - - - -
354A PHE 3.2 7.6 - - - +
355A LYS* 4.1 4.7 - - - -
359A GLY* 1.3 84.8 - - - +
361A TRP* 1.3 61.3 + - - +
362A ILE* 3.7 23.2 + - + -
377A ILE 3.5 1.9 - - - +
378A TRP* 3.2 10.0 - - - -
379A ASP* 3.1 38.6 + - + +
382A GLY* 3.8 18.6 - - - +
383A TRP* 3.1 45.3 - - + -
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Residues in contact with TRP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.6 32.1 + - + +
95A ASN 3.7 28.0 - - - -
96A GLY* 4.5 1.3 - - - -
97A TRP* 3.2 46.7 - + + -
353A SER* 3.3 9.2 - - - -
354A PHE* 2.9 35.8 + - + +
356A TYR* 3.9 13.7 - + - -
360A VAL* 1.3 70.4 - - - +
362A ILE* 1.3 62.2 + - - +
363A GLY 4.0 0.2 + - - -
376A MET* 3.9 18.7 - - + +
377A ILE* 3.3 36.6 - - - -
378A TRP* 3.6 44.2 - + + -
392A VAL* 4.4 15.5 - - + -
395A GLN* 5.1 3.4 - - + -
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Residues in contact with ILE 362 (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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317A ILE* 5.0 7.6 - - + -
319A SER* 4.3 10.1 - - - +
321A VAL* 3.5 37.2 - - + +
323A GLY* 4.4 13.0 - - - -
353A SER* 3.9 14.4 - - - +
360A VAL* 4.0 24.2 - - + +
361A TRP* 1.3 75.2 - - - +
363A GLY* 1.3 74.1 + - - +
364A ARG* 4.2 16.4 - - + -
375A GLU 3.5 1.0 - - - +
376A MET* 3.2 9.2 - - - +
377A ILE* 2.7 49.3 + - + +
379A ASP* 4.9 5.8 - - + -
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Residues in contact with GLY 363 (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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300A ARG* 5.1 2.6 + - - -
323A GLY* 4.2 6.4 - - - +
351A GLY* 5.5 0.9 - - - -
352A PHE* 3.9 25.3 + - - +
361A TRP 4.0 1.0 + - - -
362A ILE* 1.3 78.9 - - - +
364A ARG* 1.3 64.7 + - - +
374A PHE* 3.6 15.8 - - - -
375A GLU 3.4 6.5 - - - -
376A MET* 3.6 16.5 - - - +
407A SER* 5.2 0.9 + - - -
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Residues in contact with ARG 364 (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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321A VAL* 3.2 22.1 - - - +
322A PHE 3.0 25.0 + - - -
323A GLY 3.9 17.0 - - - +
327A ARG* 3.4 24.8 - - - +
330A ASP* 2.8 41.8 + - - -
362A ILE* 4.2 8.7 - - + -
363A GLY* 1.3 76.3 - - - +
365A THR* 1.3 66.5 + - - +
374A PHE* 3.1 15.7 - - - -
375A GLU* 2.8 62.1 + - + +
377A ILE* 3.8 13.0 - - + +
390A PHE* 5.9 1.2 - - - -
394A LYS* 5.0 3.2 - - - +
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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