Contacts of the helix formed by residues 25 - 33 (chain B) in PDB entry 2CKJ
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 THR 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU 3.3 10.8 + - - +
24B THR* 1.3 76.5 - - + +
26B LEU* 1.4 66.4 + - - +
27B LEU* 2.9 23.4 + - - +
28B ALA* 3.4 9.7 - - + +
29B TYR* 3.4 9.2 + - - +
72B ALA 3.5 9.9 + - - -
73B CYS* 3.9 17.1 + - - +
74B LEU* 5.0 2.7 - - - -
75B ALA 4.0 7.6 - - - -
76B PRO* 4.0 7.9 - - - -
77B ILE* 3.8 2.6 - - - +
677B GLU* 5.8 6.5 - - + +
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Residues in contact with LEU 26 (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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8B PHE* 4.7 11.0 - - + -
10B VAL* 5.6 0.2 - - + -
25B THR* 1.4 66.0 + - - +
27B LEU* 1.3 68.1 + - - +
28B ALA 3.0 0.5 + - - -
29B TYR* 2.9 19.3 + - + +
30B LEU* 3.2 29.0 + - + -
53B VAL* 4.1 15.3 - - + -
55B LEU* 5.0 2.9 - - + -
72B ALA* 3.5 25.3 + - + +
75B ALA* 2.9 24.8 + - + +
77B ILE* 3.5 15.4 - - + +
80B LEU* 3.7 28.3 - - + -
85B VAL* 4.1 22.9 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 2.9 13.7 + - - +
26B LEU* 1.3 70.6 - - - +
28B ALA* 1.3 80.5 - - + +
30B LEU* 4.3 8.1 - - + -
31B ARG* 3.4 31.2 - - + +
32B ARG* 6.3 0.4 - - - +
39B THR* 3.8 17.9 - - + +
40B LYS 4.1 9.9 - - - +
41B LEU* 3.9 26.5 - - + -
51B CYS* 4.1 4.3 - - + -
72B ALA* 2.5 33.6 + - + +
73B CYS* 3.9 24.5 - - + +
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Residues in contact with ALA 28 (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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24B THR* 5.6 4.7 - - + -
25B THR* 3.4 21.3 - - + +
26B LEU 3.0 1.0 + - - -
27B LEU* 1.3 88.1 - - + +
29B TYR* 1.3 59.8 + - - +
30B LEU 3.2 6.4 - - - +
31B ARG* 3.4 14.6 - - - +
32B ARG* 2.9 56.5 + - - +
33B LYS* 3.5 4.5 + - - +
677B GLU* 5.3 2.5 - - - +
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Residues in contact with TYR 29 (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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8B PHE* 3.9 27.4 - + - -
15B VAL* 3.8 11.7 - - + +
17B GLU* 3.1 39.1 + - + +
24B THR* 5.7 6.1 - - - -
25B THR 3.4 6.9 + - - +
26B LEU* 2.9 14.5 + - + +
28B ALA* 1.3 76.4 - - - +
30B LEU* 1.3 61.0 + - + +
33B LYS* 2.9 46.7 + - + +
34B LEU* 3.1 44.0 + - + +
77B ILE* 3.9 29.4 - - + -
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Residues in contact with LEU 30 (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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10B VAL* 4.0 31.0 - - + -
26B LEU* 3.2 39.9 + - + +
27B LEU* 4.3 6.3 - - + -
28B ALA 4.1 2.2 - - - +
29B TYR* 1.3 82.7 - - + +
31B ARG* 1.3 64.6 + - + +
34B LEU* 3.6 15.9 - - + +
35B GLY 3.4 6.4 + - - -
36B LEU* 3.2 36.8 + - + +
39B THR* 4.5 14.8 - - + +
53B VAL* 4.5 13.5 - - + -
72B ALA* 5.1 0.9 - - + -
85B VAL* 5.2 3.8 - - + -
87B THR* 4.4 15.5 - - - +
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Residues in contact with ARG 31 (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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27B LEU* 3.4 28.9 - - + +
28B ALA* 3.4 6.7 - - - +
29B TYR 3.2 0.2 - - - -
30B LEU* 1.3 79.8 - - + +
32B ARG* 1.3 75.5 + - + +
35B GLY* 3.5 16.8 - - - -
36B LEU 4.3 10.9 - - - +
37B SER* 4.2 6.2 + - - +
38B GLY 3.7 11.9 - - - +
39B THR* 2.7 28.1 + - - +
40B LYS* 4.0 12.6 - - - +
41B LEU* 5.1 8.5 - - - +
115B PHE* 6.0 1.4 - - - -
595B ASP* 3.3 32.2 + - - +
596B ASP* 2.8 31.9 + - - -
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Residues in contact with ARG 32 (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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27B LEU* 6.3 0.4 - - - +
28B ALA* 2.9 35.1 + - - +
31B ARG* 1.3 93.8 - - + +
33B LYS* 1.3 59.2 + - - +
35B GLY* 4.4 2.9 - - - +
41B LEU* 6.3 1.0 - - - +
595B ASP* 6.0 0.2 + - - -
599B ARG* 3.5 29.8 + - - +
675B THR* 5.5 0.6 - - - -
676B PRO* 3.4 27.2 - - - +
677B GLU* 2.8 29.5 + - - -
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Residues in contact with LYS 33 (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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17B GLU* 4.9 10.6 + - - -
28B ALA 3.5 1.4 + - - +
29B TYR* 2.9 57.3 + - + +
32B ARG* 1.3 75.1 - - - +
34B LEU* 1.3 58.0 + - + +
35B GLY 3.2 4.2 + - - -
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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