Contacts of the helix formed by residues 24 - 38 (chain B) in PDB entry 2CUY
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 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 2.7 25.3 + - - +
21B TYR 4.2 2.9 - - - -
22B GLU 5.4 0.2 - - - -
23B ALA* 1.3 75.3 - - - +
25B PRO* 1.3 57.3 - - - +
26B ALA* 3.4 5.2 + - - +
27B ALA* 3.2 18.8 + - - -
28B LYS* 2.7 34.8 + - - +
73B ALA* 3.4 23.0 + - - +
296B LEU* 4.9 7.4 - - - -
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.9 7.2 - - - +
24B SER* 1.3 84.8 - - - +
26B ALA* 1.3 63.5 + - - +
28B LYS* 3.6 11.8 - - + +
29B GLU* 3.0 28.1 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.2 8.4 + - - +
25B PRO* 1.3 80.7 - - - +
27B ALA* 1.3 62.9 + - - +
29B GLU* 4.1 3.2 - - - +
30B VAL* 3.3 26.1 + - - +
72B ARG* 3.8 13.5 - - + +
73B ALA* 3.9 2.2 - - - -
76B GLU* 3.1 46.4 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.8 25.8 - - + +
21B TYR* 4.5 0.7 - - - +
24B SER* 3.1 16.5 + - - +
26B ALA* 1.3 78.4 - - - +
28B LYS* 1.3 64.7 + - - +
30B VAL* 3.2 3.5 + - - +
31B LEU* 3.2 29.4 + - + +
69B ALA* 3.6 32.2 + - + +
73B ALA* 3.9 7.2 - - + +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.1 63.1 + - + +
22B GLU* 5.8 0.7 - - - -
24B SER 2.7 15.5 + - - +
25B PRO* 3.3 11.9 + - + +
27B ALA* 1.3 74.4 - - - +
29B GLU* 1.3 64.3 + - - +
31B LEU 3.5 0.2 + - - -
32B ASP* 2.7 58.5 + - - +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 3.0 17.0 + - - +
26B ALA* 4.1 4.3 - - - +
28B LYS* 1.3 89.7 + - - +
30B VAL* 1.3 65.9 + - - +
32B ASP* 3.1 23.1 - - + +
33B ARG* 3.0 35.6 + - + +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.3 16.4 + - - +
27B ALA 3.2 7.7 + - - +
29B GLU* 1.3 75.5 - - - +
31B LEU* 1.3 58.7 + - - +
33B ARG* 3.0 16.7 + - - +
34B ALA* 2.9 25.1 + - - +
65B ALA* 3.9 11.4 - - + +
68B TYR* 3.6 26.7 - - + -
69B ALA* 3.8 19.5 - - + +
72B ARG* 3.6 32.1 - - + +
104B LEU* 4.0 11.3 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 3.6 27.1 - - - +
20B LEU* 6.0 0.4 - - + -
21B TYR* 3.5 36.1 - - + +
27B ALA* 3.2 13.3 + - + +
30B VAL* 1.3 77.9 - - - +
32B ASP* 1.3 58.8 + - - +
34B ALA* 3.2 6.1 + - + +
35B GLU* 2.9 27.5 + - - +
42B LEU* 3.7 16.5 - - + +
45B MET* 4.2 17.7 - - + -
46B TRP* 4.5 5.2 - - + -
65B ALA* 3.9 36.1 - - + +
66B ALA* 4.2 2.0 - - - +
69B ALA* 4.0 10.5 - - + -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 2.6 22.9 + - - -
28B LYS* 2.7 51.4 + - - +
29B GLU* 3.1 19.1 - - - +
30B VAL 3.3 0.2 - - - -
31B LEU* 1.3 75.3 - - - +
33B ARG* 1.3 59.9 + - + +
35B GLU* 3.4 7.3 + - - +
36B ALA* 3.0 27.2 + - - +
42B LEU* 4.2 6.8 - - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.0 29.1 + - + +
30B VAL* 3.2 14.6 - - - +
32B ASP* 1.3 76.0 - - + +
34B ALA* 1.3 58.5 + - - +
36B ALA* 3.3 8.6 + - - +
37B ALA* 3.0 28.2 + - - +
68B TYR* 4.8 12.9 + - - -
103B GLU* 5.8 1.0 - - - +
104B LEU* 3.9 26.8 - - + +
105B GLU* 2.9 41.7 + - - +
108B LEU* 4.7 0.2 - - - +
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Residues in contact with ALA 34 (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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30B VAL 2.9 11.5 + - - +
31B LEU* 3.3 12.3 - - + +
32B ASP 3.2 0.2 - - - -
33B ARG* 1.3 76.2 - - - +
35B GLU* 1.3 58.6 + - - +
37B ALA* 3.3 1.4 + - - +
38B LEU* 2.9 33.1 + - - +
41B LEU* 3.9 12.5 - - + +
42B LEU* 6.0 0.9 - - + -
65B ALA* 3.8 28.5 - - + -
104B LEU* 5.2 0.9 - - + -
108B LEU* 3.7 22.1 - - + +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 2.9 7.8 + - - +
32B ASP* 3.6 7.6 - - - +
33B ARG 3.3 0.2 - - - -
34B ALA* 1.3 76.6 - - - +
36B ALA* 1.3 62.8 + - - +
38B LEU 4.3 3.1 - - - -
39B PRO* 3.0 27.0 - - - +
40B GLY* 2.9 26.6 + - - -
41B LEU* 3.3 6.4 + - - +
42B LEU* 2.9 58.3 + - + +
43B LYS 5.3 0.4 - - - -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP 3.0 14.8 + - - +
33B ARG* 3.4 12.8 - - - +
35B GLU* 1.3 80.9 - - - +
37B ALA* 1.3 61.2 + - - +
39B PRO* 3.7 11.0 - - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 3.0 15.7 + - - +
34B ALA 3.9 3.1 - - - +
36B ALA* 1.3 77.5 - - - +
38B LEU* 1.3 72.1 + - + +
39B PRO* 3.4 6.6 - - - +
105B GLU* 4.3 17.0 - - + -
108B LEU* 4.3 15.9 - - + -
109B ARG* 4.2 26.0 + - + +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA 2.9 12.5 + - - +
35B GLU 3.3 4.9 - - - +
37B ALA* 1.3 90.7 - - + +
39B PRO* 1.3 68.9 - - - +
40B GLY 3.2 0.2 + - - -
41B LEU* 3.0 25.7 + - + +
61B PRO* 3.6 34.5 - - + -
108B LEU* 3.7 29.2 - - + +
109B ARG* 4.6 15.7 - - + +
112B ARG* 3.6 38.6 + - + +
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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
------------------------------------------------------------
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