Contacts of the helix formed by residues 39 - 49 (chain B) in PDB entry 2CKH
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 5.2 3.8 - - + -
37B THR 4.5 0.2 - - - -
38B PRO* 1.3 68.3 - - - +
40B SER* 1.3 53.9 + - - +
41B LYS 3.2 2.5 - - - -
42B LEU* 3.0 22.1 + - + +
43B MET* 2.8 54.0 + - + +
66B ILE* 4.2 14.4 - - + -
68B GLU 3.4 1.6 + - - -
70B ASP* 3.0 45.4 + - + +
71B THR* 3.6 10.5 - - - +
72B PRO* 3.7 14.1 - - + -
75B LEU* 3.8 13.9 - - + -
77B MET* 4.3 8.5 - - + -
83B ILE* 4.2 23.8 - - + -
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Residues in contact with SER 40 (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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38B PRO* 3.2 9.5 - - - +
39B LEU* 1.3 76.3 - - - +
41B LYS* 1.3 64.2 + - - +
43B MET* 4.4 4.3 - - - -
44B LYS* 3.2 41.0 + - - +
68B GLU* 3.0 49.6 + - - +
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Residues in contact with LYS 41 (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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31B PHE* 5.0 13.9 - - - -
32B LYS 4.4 9.5 + - - -
33B ILE* 4.1 27.9 - - + +
37B THR* 4.9 9.0 - - + -
38B PRO* 3.7 13.8 + - + +
39B LEU 3.2 0.6 - - - -
40B SER* 1.3 78.5 - - - +
42B LEU* 1.3 67.9 + - - +
44B LYS* 4.4 1.8 - - - +
45B ALA* 3.3 27.2 + - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.9 17.3 - - + -
21B VAL* 4.3 21.1 - - + -
31B PHE* 3.8 41.9 - - + -
33B ILE* 5.4 13.9 - - + -
38B PRO 5.7 0.2 - - - +
39B LEU* 3.0 26.6 + - + +
41B LYS* 1.3 85.5 - - - +
43B MET* 1.3 78.1 + - + +
45B ALA* 2.9 7.9 + - - +
46B TYR* 2.8 25.3 + - + +
59B PHE* 5.1 6.7 - - + -
83B ILE* 5.0 5.8 - - + -
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Residues in contact with MET 43 (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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39B LEU* 2.8 37.7 + - + +
40B SER* 3.9 4.7 - - - +
42B LEU* 1.3 83.1 - - + +
44B LYS* 1.3 61.9 - - + +
46B TYR* 3.2 9.4 + - - +
47B CYS* 3.1 22.0 + - - -
54B MET* 4.3 12.8 - - - -
59B PHE* 3.7 40.4 - - + -
66B ILE* 3.7 17.7 - - + +
67B ASN* 3.4 34.8 - - - +
68B GLU* 3.6 25.1 - - - +
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Residues in contact with LYS 44 (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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40B SER* 3.2 24.6 + - - +
41B LYS* 4.5 1.8 - - - +
43B MET* 1.3 76.4 - - - +
45B ALA* 1.3 60.9 + - - +
47B CYS* 3.3 8.9 + - - +
48B GLU* 2.9 34.0 + - - +
54B MET* 4.5 13.5 - - + -
68B GLU* 3.5 24.9 + - - +
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Residues in contact with ALA 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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31B PHE* 4.2 19.2 - - + -
41B LYS* 3.3 25.1 + - - +
42B LEU* 2.9 7.7 + - - +
44B LYS* 1.3 77.6 - - - +
46B TYR* 1.3 58.7 + - - +
48B GLU* 4.4 6.5 - - - -
49B ARG* 2.9 36.5 + - + +
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Residues in contact with TYR 46 (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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21B VAL* 3.4 30.7 + - + -
23B GLY* 3.8 16.8 + - - -
27B SER* 4.1 2.6 + - - -
29B VAL* 3.6 33.4 - - + -
31B PHE* 4.2 16.1 - + + -
42B LEU* 2.8 15.7 + - + +
43B MET* 3.2 12.3 + - - +
45B ALA* 1.3 71.6 - - - +
47B CYS* 1.3 56.2 + - - +
49B ARG* 2.5 24.1 - - - +
50B GLN* 3.2 29.9 + - + +
52B LEU* 4.4 19.4 - - + +
57B ILE* 4.9 5.2 - - + -
59B PHE* 4.2 15.9 - + + -
85B VAL* 3.7 29.1 - - + +
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Residues in contact with CYS 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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43B MET 3.1 18.1 + - - -
44B LYS* 3.7 6.5 - - - +
45B ALA 3.2 0.4 - - - -
46B TYR* 1.3 76.7 - - - +
48B GLU* 1.3 70.2 + - - +
49B ARG 3.0 5.2 - - - +
51B GLY* 3.0 1.7 - - - -
52B LEU* 2.9 48.6 + - - +
53B SER 4.1 3.4 - - - +
54B MET* 3.9 36.8 - - + -
57B ILE* 4.2 15.3 - - - -
59B PHE* 4.9 0.4 - - - -
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Residues in contact with GLU 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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44B LYS* 2.9 20.6 + - - +
45B ALA* 4.0 5.5 - - - +
47B CYS* 1.3 79.0 - - - +
49B ARG* 1.3 60.8 + - - +
51B GLY* 3.6 9.4 + - - -
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Residues in contact with ARG 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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29B VAL* 4.1 27.0 - - - +
31B PHE* 5.7 6.3 - - + -
45B ALA* 2.9 17.4 + - + +
46B TYR* 2.5 33.9 - - - +
47B CYS 3.0 1.2 - - - +
48B GLU* 1.3 72.6 - - - +
50B GLN* 1.3 98.5 + - - +
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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