Contacts of the strand formed by residues 383 - 387 (chain B) in PDB entry 2G4C
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 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B ILE 2.7 9.2 + - - -
382B LYS* 1.3 78.9 - - - +
384B ALA* 1.3 76.2 + - - +
406B LEU* 4.7 3.4 - - + -
411B ILE* 3.9 24.9 - - + -
412B SER 3.3 3.9 + - - +
413B VAL* 3.3 12.9 - - + +
414B TRP* 3.0 20.7 + - - -
437B ILE* 3.5 3.1 - - - -
439B PHE* 3.4 26.5 - - + +
441B VAL* 4.0 21.8 - - + -
475B LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B VAL* 1.3 92.7 - - - +
385B LEU* 1.3 70.7 + - - +
414B TRP* 3.4 20.9 - - + -
432B TYR* 3.2 34.3 - - + -
437B ILE* 3.5 20.5 - - + +
439B PHE 3.3 5.6 + - - -
440B THR* 4.4 2.9 - - + -
441B VAL 3.6 7.4 + - - -
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ALA* 1.3 81.8 - - - +
386B ASP* 1.3 66.1 - - - +
399B CYS* 4.2 21.1 - - + +
402B LEU* 4.1 22.0 - - + -
403B PHE 4.7 0.2 - - - +
406B LEU* 5.4 2.2 - - + -
413B VAL* 3.6 21.5 - - + -
414B TRP 3.4 14.4 + - - +
415B PRO* 3.7 0.2 - - + -
416B GLY 3.3 3.5 + - - +
417B TYR* 3.3 40.9 + - + -
432B TYR* 4.8 1.2 - - - -
440B THR* 5.1 1.3 - - - -
441B VAL* 2.8 34.8 - - + +
443B VAL* 5.5 2.9 - - + -
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LEU* 1.3 76.8 - - - +
387B VAL* 1.3 75.7 + - + +
399B CYS* 4.3 2.8 - - - -
416B GLY* 2.7 35.7 - - - +
417B TYR* 3.8 6.5 - - - -
428B LEU* 3.2 28.7 - - + +
432B TYR* 3.1 25.6 + - - -
440B THR* 5.1 3.0 - - - +
441B VAL 3.4 5.5 + - - -
442B LEU* 3.8 10.2 - - + +
443B VAL* 3.1 24.9 + - - +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ASP* 1.3 81.7 - - + +
388B GLY* 1.3 60.2 + - - +
392B THR* 6.0 2.9 - - - +
395B LEU* 3.4 21.3 - - + -
396B ARG* 4.0 18.8 - - + +
399B CYS* 3.3 33.2 - - - -
417B TYR* 3.7 18.8 - - + +
422B GLN* 6.0 1.9 - - - -
442B LEU* 4.0 5.1 - - - +
443B VAL 3.2 5.6 - - - -
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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