Contacts of the strand formed by residues 44 - 49 (chain B) in PDB entry 2KH2
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 PRO 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 5.0 8.3 - - + -
37B GLN 3.2 12.6 - - - +
38B GLN* 3.9 29.2 - - + +
42B LYS 3.9 2.9 - - - +
43B ALA* 1.3 89.1 - - + +
45B GLN* 1.3 69.6 + - - +
174B LEU* 4.8 11.4 - - + -
224B TYR* 4.4 15.5 - - + -
237B TYR* 5.3 0.3 - - - -
238B TRP* 3.3 55.8 + - + +
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Residues in contact with GLN 45 (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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36B TYR* 3.3 9.0 - - - -
37B GLN* 2.8 43.2 + - + +
39B LYS* 5.5 6.5 - - - +
42B LYS* 6.0 1.6 - - - +
43B ALA* 3.0 25.3 + - - +
44B PRO* 1.3 91.4 + - - +
46B LEU* 1.3 64.7 + - - +
47B LEU* 3.4 10.6 + - + -
58B VAL* 6.4 0.2 - - + -
236B ASP 5.2 5.4 - - - +
237B TYR* 5.7 10.4 - - + +
238B TRP* 4.8 2.9 + - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.8 9.4 - - + -
35B TRP 3.6 7.2 - - - +
36B TYR* 3.6 25.4 - - + +
45B GLN* 1.3 73.4 - - - +
47B LEU* 1.3 59.4 + - - +
48B ILE 3.3 26.5 - - - +
49B TYR* 3.7 30.7 - - + -
55B ALA* 3.3 20.8 - - + +
58B VAL* 3.4 7.6 - - - +
229B ASN* 5.1 3.6 - - - +
234B TRP* 5.2 6.7 - - + +
235B PHE 3.5 24.2 - - - +
236B ASP* 3.8 30.7 + - + +
238B TRP* 5.1 0.2 - - - -
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Residues in contact with LEU 47 (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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35B TRP* 3.2 11.2 + - + +
36B TYR 5.0 0.4 - - - -
37B GLN* 3.5 52.3 - - + +
45B GLN* 3.4 10.1 + - + +
46B LEU* 1.3 77.4 - - - +
48B ILE* 1.3 76.6 + - + +
54B LEU* 3.8 0.3 - - - -
55B ALA* 3.1 24.8 + - - +
58B VAL* 3.7 34.5 - - + +
59B PRO* 5.0 2.7 - - + -
62B PHE* 4.0 26.5 - - + -
73B LEU* 5.6 2.9 - - + -
86B TYR* 3.8 14.6 - - + -
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Residues in contact with ILE 48 (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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34B THR* 3.6 0.4 - - - -
35B TRP* 2.8 51.5 + - + +
46B LEU* 3.3 7.2 - - - +
47B LEU* 1.3 92.7 - - + +
49B TYR* 1.3 66.6 + - - +
51B ALA* 3.6 25.4 - - - +
53B THR 3.6 9.9 - - - +
54B LEU* 3.7 29.8 - - + -
62B PHE* 3.8 16.8 - - + +
63B SER 4.2 0.2 - - - -
64B GLY* 3.9 15.9 - - - +
73B LEU* 3.9 23.3 - - + -
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Residues in contact with TYR 49 (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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33B LEU 4.1 0.9 - - - -
34B THR* 3.9 17.0 - - + -
46B LEU* 3.7 27.1 - - + -
48B ILE* 1.3 75.6 - - - +
50B ASN* 1.3 66.9 + - + +
51B ALA 3.1 3.8 + - - -
52B LYS 3.7 0.2 + - - -
53B THR* 2.8 58.2 + - + +
54B LEU 3.1 28.3 + - - -
55B ALA* 3.3 19.8 - - + -
56B ASP* 4.2 11.7 + - - -
229B ASN* 6.3 1.3 - - - -
230B LYS* 5.6 6.2 + - - -
234B TRP* 3.8 39.0 - + + -
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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