Contacts of the strand formed by residues 364 - 370 (chain A) in PDB entry 1UHG
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 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.9 17.3 - + - -
241A MET* 6.4 0.7 - - - -
243A VAL* 3.6 24.2 - - + -
244A LEU 3.3 16.4 - - - +
245A LEU* 3.9 12.8 - - + -
252A LEU* 4.2 4.7 - - - +
282A LEU* 4.6 5.6 - - + -
283A PRO* 4.1 10.5 - - + -
285A MET* 3.9 19.1 - - + -
360A ALA* 4.0 16.8 - - + -
362A HIS 3.3 13.9 - - - -
363A PRO* 1.3 74.7 - - - +
365A LEU* 1.3 71.6 + - - +
366A PHE* 4.1 14.8 - + + -
381A ARG* 3.6 3.6 - - - +
382A CYS* 2.9 61.9 + - + -
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Residues in contact with LEU 365 (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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15A PHE* 4.0 10.1 - - + -
243A VAL* 3.6 1.2 - - - -
244A LEU* 2.8 43.8 + - + -
252A LEU* 3.9 10.7 - - + +
255A LEU* 3.8 26.0 - - + -
256A GLU* 3.6 33.2 - - + +
259A ILE* 4.5 18.4 - - + -
364A PHE* 1.3 76.5 - - - +
366A PHE* 1.3 65.2 + - - +
379A PHE* 4.2 18.8 - - + -
380A GLY 3.4 12.8 - - - +
381A ARG* 3.8 13.9 - - + -
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Residues in contact with PHE 366 (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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28A PHE* 3.6 38.8 - + - -
241A MET* 3.5 33.0 - - + -
242A LEU 3.1 13.0 - - - +
243A VAL* 4.4 4.0 - - + -
244A LEU* 4.3 1.6 - - - -
285A MET* 3.8 21.8 - - + -
287A MET* 4.0 13.0 - - + -
334A ILE* 5.7 0.7 - - + -
364A PHE* 4.1 23.3 - + + -
365A LEU* 1.3 79.7 - - - +
367A CYS* 1.3 63.8 + - - +
368A ILE* 5.0 4.0 - - + -
378A PHE* 5.5 0.7 - - + -
379A PHE* 3.4 8.0 - - - -
380A GLY* 3.0 55.9 + - - +
381A ARG 3.9 4.0 - - - -
382A CYS 4.1 9.4 - - - -
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Residues in contact with CYS 367 (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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240A SER 3.8 0.5 - - - +
241A MET* 3.3 2.9 - - - +
242A LEU* 2.8 56.1 + - + +
244A LEU* 4.7 4.0 - - + +
264A LEU* 4.6 12.1 - - + -
366A PHE* 1.3 77.5 - - - +
368A ILE* 1.3 71.2 + - - +
369A LYS* 3.9 10.3 + - - -
376A VAL* 3.9 33.0 - - - -
378A PHE 3.3 5.2 - - - -
379A PHE* 4.0 14.6 - - + -
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Residues in contact with ILE 368 (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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28A PHE* 5.5 2.2 - - + -
180A PHE* 3.8 33.0 - - + -
234A PHE* 3.9 16.6 - - + -
239A MET* 4.6 5.4 - - + -
240A SER 3.3 9.0 - - - +
241A MET* 3.7 35.0 - - + -
332A ALA* 5.5 2.2 - - + -
334A ILE* 4.7 3.1 - - + -
366A PHE* 5.0 4.5 - - + -
367A CYS* 1.3 77.0 - - - +
369A LYS* 1.3 65.6 + - - +
376A VAL* 3.9 1.4 - - - -
377A LEU* 2.8 35.8 + - + +
378A PHE* 2.8 40.5 + - + +
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Residues in contact with LYS 369 (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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218A ARG* 5.8 1.8 - - - +
231A GLU* 3.3 16.8 + - - -
239A MET* 3.2 9.4 - - - +
240A SER* 2.9 56.7 + - - +
242A LEU* 4.0 32.7 - - + +
264A LEU* 6.4 0.4 - - + -
268A THR* 4.7 15.0 + - - -
273A MET* 5.5 0.4 - - - +
367A CYS* 4.4 9.4 - - - -
368A ILE* 1.3 76.7 - - - +
370A HIS* 1.3 64.9 + - - +
371A ILE* 3.6 8.5 + - - +
374A ASN* 4.0 25.9 + - - +
375A ALA 3.4 13.7 - - - +
376A VAL* 4.8 0.7 - - + -
377A LEU* 4.1 4.9 - - - -
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Residues in contact with HIS 370 (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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86A ILE* 4.4 11.4 - - + +
89A GLN* 2.8 37.5 + - - -
90A ILE* 4.3 17.9 - - + -
238A THR* 3.6 15.1 + - - -
239A MET* 5.0 2.5 - - + -
369A LYS* 1.3 71.2 - - - +
371A ILE* 1.3 59.8 + - - +
372A ALA* 3.8 23.3 - - + -
373A THR* 2.9 40.1 + - + +
374A ASN* 2.8 33.1 + - - -
375A ALA* 2.9 13.7 + - + +
377A LEU* 3.9 20.7 - - + +
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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
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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