Contacts of the strand formed by residues 382 - 387 (chain A) in PDB entry 1Y24
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A GLN* 3.6 4.2 - - + +
381A LEU* 1.3 77.2 - - + +
383A ARG* 1.3 62.0 + - - +
384A LYS* 3.5 4.2 + - + +
393A LEU* 3.2 28.2 - - - -
394A ALA* 3.3 35.4 + - + +
395A LEU 5.1 4.3 - - - +
396A LEU* 5.8 3.1 - - + +
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Residues in contact with ARG 383 (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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43A LEU* 3.8 18.6 - - - +
44A ARG* 4.3 23.8 - - - +
45A ARG* 3.1 55.8 - - + +
46A PHE 3.8 0.4 + - - -
47A TRP* 3.4 47.3 - - - +
48A ARG 3.3 21.8 - - - +
49A SER* 4.5 4.9 + - - +
328A GLN* 4.4 4.0 + - - -
379A VAL* 4.3 6.3 - - - +
380A GLN 4.7 2.8 + - - -
381A LEU 3.1 12.6 + - - +
382A LEU* 1.3 69.9 - - - +
384A LYS* 1.3 61.0 + - - +
386A VAL* 5.4 0.4 - - - -
393A LEU* 3.3 21.4 - - + +
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Residues in contact with LYS 384 (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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40A LEU 4.6 4.7 + - - -
41A TRP* 3.4 37.2 - - + +
42A PRO 2.9 29.0 - - - +
43A LEU* 3.5 2.7 + - + +
382A LEU* 3.5 5.8 + - + +
383A ARG* 1.3 74.4 - - - +
385A PRO* 1.4 80.7 + - + +
386A VAL* 3.1 10.5 - - - +
392A LEU* 3.2 17.8 + - + +
393A LEU* 3.9 0.6 - - - +
394A ALA* 5.6 5.6 - - + +
400A GLN* 5.8 3.8 - - + +
423A SER* 3.1 15.9 + - - +
424A ALA* 2.9 45.2 + - - +
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Residues in contact with PRO 385 (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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40A LEU 4.3 5.6 - - - +
42A PRO* 3.7 20.9 - - + -
45A ARG* 3.3 7.4 + - - -
384A LYS* 1.4 108.4 - - + +
386A VAL* 1.3 58.2 + - - +
390A MET* 4.0 13.7 - - + -
391A GLY* 3.3 6.4 - - - -
392A LEU* 3.0 63.5 + - + +
402A TRP* 4.7 3.8 - - + -
421A LEU* 4.8 6.7 - - + -
423A SER* 4.9 3.1 - - - +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 3.2 22.8 - - + +
43A LEU 3.3 27.8 - - - +
44A ARG 3.2 16.2 - - - +
45A ARG* 3.3 31.6 - - + +
383A ARG 5.4 0.2 - - - -
384A LYS 3.1 21.1 - - - +
385A PRO* 1.3 74.3 - - - +
387A LEU* 1.3 73.5 + - + +
390A MET* 3.3 15.4 - - - +
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Residues in contact with LEU 387 (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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45A ARG* 4.4 3.0 - - - +
46A PHE* 3.7 21.4 - - + +
325A VAL* 5.2 1.4 - - - +
386A VAL* 1.3 82.7 - - + +
388A THR* 1.3 81.8 + - + +
389A ALA* 3.0 5.8 + - + +
390A MET* 2.7 50.7 + - + +
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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