Contacts of the strand formed by residues 436 - 440 (chain A) in PDB entry 4E1O
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 ILE 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA* 3.9 7.9 - - + +
80A TYR* 3.6 39.9 - - + +
248A THR* 6.4 0.2 - - + -
424A LEU* 4.7 5.2 - - - -
434A PHE* 3.8 20.0 - - + -
435A LEU* 1.3 81.0 - - - +
437A PRO* 1.3 81.9 - - + +
446A ILE* 4.0 1.3 - - - +
447A ARG* 3.0 50.9 + - - +
334B TYR* 3.5 31.9 - - + +
336B ARG 5.7 4.5 - - - +
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Residues in contact with PRO 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.7 22.9 - - + -
435A LEU 4.9 0.2 - - - +
436A ILE* 1.3 94.1 - - + +
438A ALA* 1.3 60.4 + - - +
444A LEU* 3.7 22.4 - - + -
445A ILE 3.2 15.7 - - - +
446A ILE* 4.5 0.7 - - - -
447A ARG* 4.4 2.5 - - - -
333B ILE* 4.7 17.3 - - + +
334B TYR* 3.4 25.6 - - - +
336B ARG 5.6 4.9 - - - +
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Residues in contact with ALA 438 (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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249A GLY* 4.0 17.9 - - - -
437A PRO* 1.3 75.0 - - - +
439A THR* 1.3 65.9 + - - +
444A LEU* 3.5 10.6 - - - +
445A ILE* 2.9 40.5 + - + +
447A ARG* 3.9 20.3 - - - +
333B ILE* 3.8 13.0 - - + -
334B TYR* 4.7 8.7 - - + -
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Residues in contact with THR 439 (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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192A GLN* 4.8 6.4 + - - +
249A GLY* 5.8 2.1 - - - -
438A ALA* 1.3 80.3 + - - +
440A ILE* 1.3 67.8 + - - +
441A GLN 3.2 28.2 + - - +
442A ASP* 4.7 2.2 - - - -
443A LYS 3.4 13.1 + - - +
444A LEU* 4.6 3.2 - - - +
445A ILE* 4.7 1.1 - - - -
333B ILE* 3.5 31.5 - - - +
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLN* 4.2 15.3 - - - +
217A PHE* 4.2 28.9 - - + -
250A VAL* 3.5 27.6 - - + -
401A PRO* 3.5 48.5 - - + +
402A ALA* 4.8 0.2 - - + -
410A VAL* 5.1 0.2 - - + -
439A THR* 1.3 76.4 - - - +
441A GLN* 1.3 67.5 + - + +
443A LYS* 2.9 33.6 + - + +
445A ILE* 3.9 22.4 - - + -
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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