Contacts of the strand formed by residues 359 - 364 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H LYS* 3.7 0.7 - - - -
356H TYR 3.0 27.2 + - - -
357H GLY 3.9 1.0 - - - +
358H ASN* 1.3 80.2 - - - +
360H VAL* 1.3 70.7 + - - +
378H TRP* 3.7 11.7 - - - -
379H ASP 3.1 4.7 - - - -
380H PRO* 3.7 5.2 - - - -
381H ASN* 3.1 18.8 + - - +
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Residues in contact with VAL 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H ILE* 4.6 5.2 - - + -
353H SER* 5.2 4.0 - - - -
354H PHE 3.3 7.2 - - - +
355H LYS* 4.0 6.5 - - - -
359H GLY* 1.3 81.6 - - - +
361H TRP* 1.3 63.9 + - - +
362H ILE* 3.7 23.0 + - + +
377H ILE 3.7 1.4 - - - +
378H TRP* 3.3 9.2 - - - -
379H ASP* 3.0 33.2 + - + +
382H GLY* 3.7 24.9 - - - +
383H TRP* 3.1 44.0 - - + -
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Residues in contact with TRP 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H ILE* 3.6 24.3 + - + +
95H ASN* 3.7 29.6 - - - -
96H GLY* 4.5 1.6 - - - -
97H TRP* 3.3 43.5 - + + -
352H PHE* 5.3 0.2 - - - -
353H SER* 3.3 10.2 - - - -
354H PHE* 2.8 35.6 + - + +
356H TYR* 3.9 21.3 - + - -
360H VAL* 1.3 73.1 - - - +
362H ILE* 1.3 59.4 + - - +
376H MET* 3.9 23.2 - - + +
377H ILE 3.4 23.6 - - - -
378H TRP* 3.6 53.1 - + + -
392H VAL* 4.4 15.3 - - + -
395H GLN* 5.0 2.7 - - + -
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Residues in contact with ILE 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H ARG* 6.2 0.7 - - - +
317H ILE* 4.7 10.3 - - + -
319H SER* 4.3 10.1 - - - +
321H VAL* 3.6 34.3 - - + +
323H GLY* 4.3 19.7 - - - +
352H PHE 5.0 0.2 - - - +
353H SER* 3.9 13.9 - - - +
360H VAL* 4.0 27.1 - - + +
361H TRP* 1.3 78.3 - - - +
363H GLY* 1.3 73.6 + - - +
364H ARG* 4.0 9.2 + - + +
375H GLU 3.6 1.2 - - - +
376H MET* 3.5 7.1 - - - -
377H ILE* 2.8 43.3 + - + +
379H ASP* 5.0 4.3 - - + -
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Residues in contact with GLY 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300H ARG* 4.8 5.2 + - - -
323H GLY 4.3 5.5 - - - +
351H GLY* 5.2 1.4 - - - -
352H PHE* 3.7 28.2 + - - +
361H TRP 4.2 0.4 + - - -
362H ILE* 1.3 77.1 - - - +
364H ARG* 1.3 63.8 + - - +
374H PHE* 3.7 13.8 - - - -
375H GLU 3.5 6.7 - - - -
376H MET* 3.6 16.6 - - - +
407H SER* 5.0 1.2 + - - -
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Residues in contact with ARG 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321H VAL* 3.2 14.6 - - - +
322H PHE 3.0 27.5 + - - -
323H GLY* 3.8 20.2 - - - +
327H ARG* 3.3 24.2 - - - +
330H ASP* 3.1 38.4 + - - -
362H ILE* 4.5 4.9 - - + +
363H GLY* 1.3 76.6 - - - +
365H THR* 1.3 64.2 + - - +
374H PHE* 3.1 15.9 - - - -
375H GLU* 2.7 69.1 + - + +
377H ILE* 3.4 21.9 - - + +
390H PHE* 5.1 1.8 - - - -
394H LYS* 4.6 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
------------------------------------------------------------
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