Contacts of the strand formed by residues 40 - 44 (chain A) in PDB entry 1KOJ
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 2.6 45.0 + - - -
37A ASN* 4.0 14.2 + - - +
38A HIS 3.6 2.2 + - - +
39A PHE* 1.3 76.7 - - - +
41A LEU* 1.3 64.4 + - - +
42A THR* 5.6 0.5 + - - -
51A LEU* 4.3 5.4 - - - +
52A LEU 3.3 13.7 - - - -
53A ASP* 3.9 10.5 - - - -
54A TYR* 3.7 8.5 + - - -
313A LYS* 5.1 4.7 + - - +
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Residues in contact with LEU 41 (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 SER* 1.3 77.7 - - - +
42A THR* 1.3 61.8 + - - +
43A LEU* 3.4 36.1 - - + -
50A ILE 4.5 0.4 - - - +
51A LEU* 3.5 3.3 - - - +
52A LEU* 3.0 50.1 + - + +
54A TYR* 5.0 0.9 - - + -
313A LYS* 3.7 41.7 - - + +
315A ALA* 4.0 14.8 - - + +
318A LEU* 3.5 31.0 - - + -
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Residues in contact with THR 42 (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 SER* 5.6 0.5 + - - -
41A LEU* 1.3 74.0 - - - +
43A LEU* 1.3 67.6 + - - +
44A ASN 4.0 1.2 + - - -
49A HIS* 4.1 20.4 - - + -
50A ILE 3.6 5.6 - - - +
51A LEU* 3.7 13.7 - - - +
313A LYS* 5.1 6.8 + - - +
547B PHE* 4.1 26.9 - - + -
550B GLN* 5.8 1.3 - - - +
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Residues in contact with LEU 43 (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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41A LEU* 3.4 33.2 - - + -
42A THR* 1.3 77.8 - - - +
44A ASN* 1.3 61.5 + - - +
45A THR* 3.6 2.5 + - + +
48A GLY 4.0 0.2 - - - +
49A HIS* 3.2 7.0 - - - -
50A ILE* 2.8 55.2 + - + +
52A LEU* 6.1 0.2 - - + -
301A TRP* 3.6 32.3 - - + -
302A MET* 4.1 15.5 - - + -
305A HIS* 3.5 32.8 - - + +
313A LYS* 5.2 3.1 - - - +
315A ALA* 4.2 8.1 - - + -
492A MET* 5.8 1.3 - - - -
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Residues in contact with ASN 44 (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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42A THR 4.0 2.8 + - - -
43A LEU* 1.3 71.2 - - - +
45A THR* 1.3 61.5 + - - +
46A ASN* 2.9 37.6 + - - +
48A GLY 4.1 1.4 + - - +
49A HIS* 3.3 43.1 + - + +
301A TRP* 3.6 13.0 + - - -
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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