Contacts of the helix formed by residues 23 - 32 (chain F) in PDB entry 1CVJ
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 23 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP 3.6 5.4 + - - +
22F VAL* 1.3 84.7 - - - +
24F GLU* 1.3 62.2 + - - +
25F ALA* 3.2 13.8 - - + +
26F MET* 3.0 35.2 + - - +
27F LEU* 2.9 23.7 + - - +
42F VAL* 4.4 2.5 - - - -
20H PRO 5.4 2.2 - - - +
21H ASP* 4.3 17.6 + - + +
23H THR* 3.7 29.4 - - + -
44H ARG* 6.0 4.3 - - - -
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Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F THR* 1.3 73.9 - - - +
25F ALA* 1.3 52.6 + - - +
27F LEU* 3.4 4.2 - - - +
28F TYR* 2.6 37.9 + - - +
40F ILE* 3.6 27.0 - - + +
41F ARG* 3.9 0.8 - - - -
42F VAL* 3.2 33.7 + - + +
44F ARG* 3.2 24.9 + - - +
44H ARG* 3.5 15.9 + - - +
49H ARG* 3.0 44.8 + - + -
7R A 3.6 12.7 - - - +
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F THR* 3.2 13.0 - - - +
24F GLU* 1.3 78.6 - - - +
26F MET* 1.3 63.7 + - + +
28F TYR* 3.2 4.5 + - - +
29F GLU* 3.1 30.3 + - - +
20H PRO 5.6 4.9 - - - +
21H ASP* 6.0 0.9 - - - +
44H ARG* 5.6 0.9 - - - +
48H THR 3.8 14.0 - - - +
49H ARG* 3.6 22.1 + - - +
50H ARG* 4.1 9.2 - - - -
51H SER 4.9 2.2 - - - +
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Residues in contact with MET 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP 4.0 7.6 - - - +
22F VAL* 3.4 33.4 - - + -
23F THR* 3.0 29.5 + - - +
25F ALA* 1.3 74.7 - - + +
27F LEU* 1.3 66.2 + - - +
29F GLU* 3.4 16.4 + - - +
30F LYS* 3.1 20.6 + - - +
77F ILE* 4.3 10.8 - - + +
78F LYS* 3.5 30.5 - - + -
21H ASP* 4.3 18.2 - - - +
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 4.3 16.4 - - + -
18F LEU* 4.3 7.4 - - + -
22F VAL* 3.9 12.3 - - + -
23F THR 2.9 12.4 + - - +
24F GLU* 3.4 9.9 - - - +
26F MET* 1.3 73.3 - - - +
28F TYR* 1.3 66.0 + - - +
30F LYS* 3.0 5.7 + - - +
31F PHE* 3.0 54.0 + - + +
40F ILE* 4.0 15.0 - - + -
42F VAL* 3.3 34.8 - - + -
55F ALA* 3.5 15.9 - - + -
57F VAL* 4.5 1.1 - - + -
77F ILE* 4.3 16.4 - - + -
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLU 2.6 20.3 + - - +
25F ALA 3.4 5.6 - - - +
27F LEU* 1.3 73.3 - - - +
29F GLU* 1.3 64.5 + - + +
32F SER* 2.6 57.3 + - - +
37F ILE* 3.8 24.7 - - + -
40F ILE* 4.6 9.4 - - + +
90G ASP* 2.5 40.3 + - - -
91G PRO* 4.1 0.5 - - - +
92G SER* 3.8 9.4 + - - -
47H ILE* 3.6 21.3 - - + -
48H THR* 3.5 45.7 - - + +
49H ARG* 4.8 2.7 - - + -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ALA* 3.1 16.0 + - - +
26F MET* 3.7 16.8 - - - +
27F LEU 3.3 0.2 - - - -
28F TYR* 1.3 84.8 - - + +
30F LYS* 1.3 62.8 + - - +
32F SER* 4.3 4.9 - - - -
33F PRO* 3.3 17.2 - - - +
95G LYS* 5.6 2.8 + - - -
50H ARG* 4.8 11.8 + - - -
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F MET 3.1 12.0 + - - +
27F LEU* 3.0 12.9 + - - +
29F GLU* 1.3 79.6 - - - +
31F PHE* 1.3 73.6 + - + +
33F PRO* 3.2 14.7 - - - +
72F MET* 2.9 57.7 - - - +
75F ASP* 3.0 28.3 + - - -
76F VAL 4.6 7.2 - - - +
77F ILE* 3.9 28.0 - - + -
82F VAL* 6.1 1.6 - - + -
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Residues in contact with PHE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 5.1 3.4 - - + -
15F VAL* 4.1 12.8 - - + -
27F LEU* 3.0 43.0 + - + +
30F LYS* 1.3 83.7 - - + +
32F SER* 1.3 64.7 + - - +
33F PRO 3.1 3.8 - - - -
34F ALA* 3.0 13.4 + - - +
37F ILE* 3.8 4.7 - - + -
57F VAL* 3.6 33.0 - - + -
59F PHE* 3.4 28.6 - + + -
68F ALA* 3.9 15.5 - - + -
72F MET* 3.8 24.7 - - + -
77F ILE* 5.2 0.7 - - + -
82F VAL* 5.0 3.8 - - + -
84F ILE* 3.4 38.6 - - + -
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F TYR* 2.6 57.7 + - - -
29F GLU* 4.3 3.1 - - - -
31F PHE* 1.3 70.5 - - - +
33F PRO* 1.3 68.1 - - - +
35F GLY 3.4 16.5 + - - +
37F ILE* 3.6 12.7 - - - +
90G ASP* 4.7 0.7 + - - +
92G SER* 3.8 20.4 + - - -
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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