Contacts of the strand formed by residues 376 - 380 (chain A) in PDB entry 1GPU
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 LEU 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU* 4.6 7.9 - - + +
369A VAL* 4.4 15.7 - - + -
370A TYR* 3.9 28.5 - - + -
373A LEU* 2.9 25.3 + - + +
375A GLU* 1.3 78.6 - - - +
377A ILE* 1.3 61.4 + - - +
378A GLY 4.1 0.2 - - - -
391A TRP* 4.1 6.7 - - + -
410A ARG* 3.0 27.2 + - - +
436A LYS* 3.5 17.9 - - + +
438A TYR* 3.6 32.3 - - + -
464A ILE* 5.8 0.7 - - + -
515A LEU* 4.0 27.8 - - + -
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Residues in contact with ILE 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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134A ASN* 4.3 12.1 - - + +
374A PRO 4.5 4.3 - - - +
375A GLU 3.6 10.5 - - - +
376A LEU* 1.3 83.1 - - - +
378A GLY* 1.3 59.0 + - - +
397A PHE* 5.9 1.8 - - + -
409A GLY 5.4 0.9 - - - +
410A ARG* 3.5 38.6 - - + +
412A ILE* 3.8 29.0 - - + +
428A ILE* 4.9 7.9 - - + -
435A TYR* 3.6 29.6 - - + -
436A LYS 3.0 7.8 + - - +
437A PRO* 3.1 12.2 - - + +
438A TYR* 2.9 26.6 + - - +
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Residues in contact with GLY 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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376A LEU 4.1 1.0 + - - -
377A ILE* 1.3 75.6 - - - +
379A GLY* 1.3 59.2 + - - -
391A TRP* 4.5 2.0 - - - -
410A ARG 3.0 9.5 + - - +
411A TYR* 3.4 10.4 - - - -
412A ILE* 2.8 28.2 + - - +
414A TYR* 5.0 0.9 - - - -
438A TYR* 3.4 37.7 - - - -
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Residues in contact with GLY 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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378A GLY* 1.3 75.0 - - - -
380A SER* 1.3 62.3 + - - -
389A THR* 3.8 8.0 + - - +
411A TYR* 3.4 17.1 - - - -
412A ILE 3.1 16.6 - - - -
414A TYR* 4.1 11.4 - - - -
438A TYR* 3.3 5.3 + - - -
439A GLY* 3.4 3.4 - - - -
440A GLY 2.9 20.6 + - - -
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Residues in contact with SER 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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379A GLY* 1.3 72.4 - - - -
381A ALA* 1.3 62.2 + - - +
382A ASP 3.0 6.6 + - - -
383A LEU* 3.1 16.3 + - - +
384A THR* 3.7 12.6 - - - -
387A ASN* 2.8 22.9 + - - -
389A THR* 3.6 8.3 - - - -
411A TYR* 3.2 19.6 + - - -
412A ILE 3.2 5.6 + - - +
413A ARG* 4.1 2.1 - - - -
414A TYR* 3.2 26.4 + - - -
421A MET* 4.1 1.8 - - - -
440A GLY 3.4 7.9 - - - +
192B ASP* 4.6 1.6 - - - +
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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