Contacts of the strand formed by residues 352 - 356 (chain G) 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 PHE 352 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279G SER* 3.7 10.5 - - - -
290G VAL* 3.9 11.2 - - - +
300G ARG* 4.1 6.1 - - - +
351G GLY* 1.3 74.8 - - - +
353G SER* 1.3 78.5 + - - +
354G PHE* 3.9 22.7 - + - -
361G TRP 5.0 0.4 - - - -
362G ILE* 5.0 0.5 - - - +
363G GLY* 3.9 22.7 + - - +
374G PHE* 4.0 11.0 - + - -
376G MET* 3.7 30.7 - - + -
407G SER* 3.5 20.9 - - - -
408G GLY 3.8 9.6 - - - -
409G SER* 3.7 25.4 - - - +
422G PHE* 3.5 41.7 - + + -
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Residues in contact with SER 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G SER 5.6 0.2 - - - +
281G TYR* 3.4 20.8 + - - -
290G VAL* 3.5 21.0 - - - +
300G ARG* 4.9 2.6 - - - -
317G ILE* 3.7 30.7 - - - +
352G PHE* 1.3 86.5 + - - +
354G PHE* 1.3 67.8 + - - +
360G VAL* 5.2 2.5 - - - -
361G TRP 3.4 14.4 + - - -
362G ILE* 3.9 16.3 - - - +
383G TRP* 5.1 2.2 - - - -
409G SER* 5.7 0.3 - - - -
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Residues in contact with PHE 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.3 5.8 - - + -
97G TRP* 3.6 27.4 - + - -
281G TYR* 3.7 42.4 - + + -
352G PHE* 3.9 20.4 - + - -
353G SER* 1.3 73.8 - - - +
355G LYS* 1.3 60.4 + - - +
356G TYR* 3.9 19.6 + - + -
360G VAL* 3.2 8.6 - - - +
361G TRP* 2.9 38.9 + - + -
409G SER* 3.5 17.5 - - - -
410G PHE 4.5 2.5 - - - -
411G VAL* 5.6 0.9 - - + -
420G PRO* 3.6 28.7 - - + -
421G CYS 3.4 27.6 - - - -
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Residues in contact with LYS 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.0 12.7 - - - +
281G TYR* 3.0 19.3 + - - +
283G ASN* 5.6 1.9 + - - -
288G THR* 5.1 4.9 - - + +
353G SER 4.1 0.4 + - - -
354G PHE* 1.3 72.8 - - - +
356G TYR* 1.3 66.7 + - - +
357G GLY* 2.4 39.3 + - - +
358G ASN* 4.8 2.6 + - - +
359G GLY 3.7 5.2 - - - +
360G VAL* 4.2 0.7 - - - -
383G TRP* 3.3 61.5 - - + +
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Residues in contact with TYR 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 3.6 29.1 - - + +
92G CYS 2.7 32.2 + - - -
93G PRO* 4.2 8.1 - - + -
94G ILE* 3.8 11.2 - - + +
354G PHE* 3.9 23.5 + + + -
355G LYS* 1.3 75.5 - - - +
357G GLY* 1.3 59.0 - - - +
358G ASN 3.0 0.7 + - - -
359G GLY* 2.8 29.7 + - - +
361G TRP* 4.2 24.9 - + - -
378G TRP* 4.0 19.4 - + + -
420G PRO* 3.3 21.7 - - - +
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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