Contacts of the strand formed by residues 376 - 382 (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 VAL 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER* 3.0 11.9 + - - +
8A MET* 3.1 41.5 - - + -
11A CYS* 4.0 15.7 - - + -
12A PHE* 5.9 0.9 - - + -
31A PRO* 4.0 18.4 - - + +
32A ILE* 3.7 23.2 + - - +
264A LEU* 5.5 0.4 - - + -
367A CYS* 3.9 21.3 - - - -
368A ILE 4.0 2.0 - - - -
369A LYS* 4.6 2.2 - - + +
374A ASN 4.6 0.7 - - - +
375A ALA* 1.3 71.6 - - - +
377A LEU* 1.3 63.9 + - - +
378A PHE 3.5 26.7 - - - +
379A PHE* 4.3 0.7 - - + -
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Residues in contact with LEU 377 (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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30A CYS* 3.2 33.1 - - - -
31A PRO* 3.4 3.1 - - - +
32A ILE* 4.0 23.8 - - + -
86A ILE* 4.2 16.2 - - + -
90A ILE* 4.1 16.4 - - + -
99A PHE* 5.3 1.1 - - + -
239A MET* 3.7 38.1 - - + -
368A ILE* 2.8 13.6 + - + +
369A LYS 4.1 2.0 - - - -
370A HIS* 3.9 35.4 - - + +
375A ALA* 4.7 2.5 - - + +
376A VAL* 1.3 76.1 - - - +
378A PHE* 1.3 77.3 + - + +
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Residues in contact with PHE 378 (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* 3.3 40.8 - + + -
29A TYR 3.4 9.2 - - - -
30A CYS* 3.7 22.2 - - + -
31A PRO* 3.9 0.4 - - - -
99A PHE* 3.6 30.1 - + - -
178A ILE* 3.7 17.0 - - + -
180A PHE* 3.5 37.9 - + + -
330A ALA* 4.5 0.2 - - + -
331A HIS 5.0 2.0 - - - -
366A PHE* 5.5 1.6 - - + -
367A CYS* 3.3 4.0 - - - -
368A ILE* 2.8 52.5 + - + -
376A VAL* 3.5 9.5 - - - +
377A LEU* 1.3 91.4 - - + +
379A PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 379 (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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11A CYS* 3.4 29.2 - - - -
12A PHE* 3.7 29.8 - + - -
15A PHE* 3.6 37.7 - + + -
28A PHE* 3.5 7.0 - - - -
29A TYR* 3.1 53.6 + + + +
31A PRO* 4.2 0.4 - - + +
244A LEU* 5.5 2.2 - - + -
259A ILE* 4.7 5.4 - - + -
264A LEU* 5.9 1.1 - - + -
365A LEU* 4.2 26.7 - - + -
366A PHE* 3.4 17.0 - - - -
367A CYS* 4.0 19.7 - - + -
376A VAL* 4.3 0.7 - - + -
378A PHE* 1.3 73.6 - - - +
380A GLY* 1.3 75.1 + - - +
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Residues in contact with GLY 380 (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* 5.2 0.2 - - - -
27A ILE* 2.9 17.0 - - - -
28A PHE* 4.2 0.2 - - - -
365A LEU* 3.4 9.3 - - - +
366A PHE* 3.0 46.0 + - - +
379A PHE* 1.3 87.7 - - - +
381A ARG* 1.3 60.0 + - - -
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Residues in contact with ARG 381 (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* 4.5 4.2 - - + -
19A LYS* 3.8 23.4 + - - +
22A HIS 3.0 22.0 + - - -
23A ALA* 4.8 4.6 - - - +
24A ASN* 3.7 7.7 - - - +
25A GLU 2.9 32.0 + - - +
26A ASN* 3.3 8.1 - - - +
27A ILE* 2.8 52.0 + - + +
252A LEU* 3.7 17.4 - - + +
256A GLU* 2.8 40.0 + - - +
287A MET* 3.8 2.3 - - - +
364A PHE 3.6 4.3 - - - +
365A LEU* 3.8 10.3 - - + -
366A PHE* 4.1 2.0 - - - -
380A GLY* 1.3 74.7 - - - -
382A CYS* 1.3 60.7 + - - +
383A VAL* 3.5 17.7 - - + -
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Residues in contact with CYS 382 (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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26A ASN* 3.4 4.5 - - - -
198A PHE* 4.3 2.1 - - - -
285A MET* 4.1 17.3 - - + -
287A MET* 4.5 4.5 - - + -
363A PRO* 3.2 23.7 - - - +
364A PHE* 2.9 48.0 + - + -
366A PHE* 4.1 4.1 - - + -
381A ARG* 1.3 72.6 - - - +
383A VAL* 1.3 62.5 + - - +
384A SER 4.1 1.6 - - - -
385A PRO* 3.6 41.7 - - - -
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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