Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 1CW0
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA* 3.5 23.8 - - + +
20A ARG 4.4 3.4 - - - +
21A ASP* 1.3 79.4 - - - +
23A ALA* 1.3 61.2 + - - +
24A ILE* 3.8 1.2 - - - +
25A GLU* 3.2 19.5 + - - +
26A LYS* 2.9 29.0 + - - +
354O T 3.3 25.4 - - - +
355O A 2.7 38.1 + - - +
356O G 3.8 13.0 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 1.3 73.5 - - - +
24A ILE* 1.3 64.6 + - + +
26A LYS* 3.3 10.9 + - - +
27A ARG* 3.1 22.9 + - - +
120A ARG* 4.8 20.0 - - + +
355O A 4.9 2.0 - - - -
356O G 3.1 17.9 + - - +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.8 0.9 - - - +
23A ALA* 1.3 76.8 - - + +
25A GLU* 1.3 63.6 + - - +
27A ARG* 3.6 2.3 + - - +
28A LEU* 3.1 24.1 + - - +
63A THR* 3.7 19.2 - - - +
64A HIS 3.7 30.5 - - - +
65A GLY 3.7 2.7 - - - +
116A GLU* 3.6 36.6 - - + +
119A LEU* 3.5 24.8 - - + +
120A ARG* 3.9 17.0 - - + -
355O A 3.5 34.1 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR 4.4 0.3 - - - +
20A ARG* 3.8 9.9 - - - +
21A ASP* 2.9 29.2 + - - +
22A THR* 3.2 25.6 + - - +
24A ILE* 1.3 76.7 - - - +
26A LYS* 1.3 60.7 + - - +
29A ALA* 2.9 31.6 + - - +
41A VAL* 6.1 0.3 - - - +
42A GLN* 3.4 17.5 - - - +
51A ASP* 3.3 23.7 - - - +
52A PHE* 3.3 18.8 - - + -
63A THR* 3.1 22.2 - - - +
203A MG 4.2 4.7 - - - -
354O T 4.2 5.5 - - - +
355O A 4.2 3.2 + - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.3 33.3 + - + +
22A THR 2.9 17.8 + - - +
23A ALA* 3.3 8.0 + - - +
25A GLU* 1.3 77.2 - - - +
27A ARG* 1.3 62.1 + - - +
29A ALA* 3.6 6.0 - - - +
30A SER* 3.0 24.6 + - - -
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.1 15.4 + - - +
24A ILE* 4.1 4.7 - - - +
26A LYS* 1.3 76.5 - - - +
28A LEU* 1.3 59.4 + - - +
30A SER* 3.3 6.5 + - - -
31A LEU* 2.9 39.1 + - + +
119A LEU* 2.6 50.9 + - + +
124A LYS* 4.2 9.2 - - - +
125A LEU 3.3 21.8 + - - -
126A THR* 4.4 0.6 - - - +
127A ASP* 2.6 35.4 + - - +
130A LEU* 3.2 27.5 - - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE 3.1 17.7 + - - +
27A ARG* 1.3 77.6 - - - +
29A ALA* 1.3 63.1 + - - +
31A LEU* 3.1 10.7 + - + +
32A LEU* 2.8 38.4 + - + +
52A PHE* 3.3 29.6 - - + -
61A ILE* 3.6 21.3 - - + -
63A THR* 3.3 25.4 - - + -
114A VAL* 4.5 8.1 - - + -
119A LEU* 4.7 8.7 - - + +
134A LEU* 3.8 36.8 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 2.9 18.4 + - - +
26A LYS* 3.6 7.6 - - - +
27A ARG 3.3 0.2 - - - -
28A LEU* 1.3 76.2 - - - +
30A SER* 1.3 52.7 + - - +
32A LEU* 3.2 1.1 + - - -
33A THR* 2.8 40.1 + - - +
39A PHE* 3.7 15.6 - - + -
52A PHE* 3.7 20.3 - - + -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS 3.0 18.2 + - - -
27A ARG* 3.5 6.7 - - - -
29A ALA* 1.3 77.1 - - - +
31A LEU* 1.3 58.2 + - - +
33A THR* 3.4 7.1 + - - -
34A GLY* 3.0 25.5 + - - -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 2.9 33.7 + - + +
28A LEU* 3.1 11.2 + - + +
30A SER* 1.3 77.4 - - - +
32A LEU* 1.3 62.5 + - - +
34A GLY* 3.3 3.2 + - - -
35A GLN* 3.2 22.8 + - - +
119A LEU* 4.3 5.2 - - + -
127A ASP* 3.8 33.9 - - - +
130A LEU* 3.8 31.2 - - + -
131A THR* 3.7 26.3 + - - +
134A LEU* 4.1 19.7 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 2.8 29.5 + - + +
31A LEU* 1.3 72.3 - - - +
33A THR* 1.3 64.9 + - - +
35A GLN* 3.0 17.9 + - - +
36A GLY 3.3 7.8 + - - -
37A LEU* 3.3 23.1 + - + +
39A PHE* 3.7 26.5 - - + -
52A PHE* 3.6 37.7 - - + -
54A VAL* 5.3 2.9 - - + -
61A ILE* 4.4 10.3 - - + -
134A LEU* 4.4 15.0 - - + -
138A ILE* 3.8 29.8 - - + -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 2.8 23.9 + - - -
30A SER* 3.8 7.9 - - - -
32A LEU* 1.3 73.0 - - - +
34A GLY* 1.3 58.0 + - - +
36A GLY* 2.9 20.7 + - - +
37A LEU 4.7 4.7 - - - -
39A PHE* 3.6 16.1 - - - -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER 3.0 14.7 + - - -
31A LEU* 3.8 4.7 - - - -
32A LEU 3.3 0.2 - - - -
33A THR* 1.3 78.1 - - - +
35A GLN* 1.3 57.6 + - - +
36A GLY* 3.2 1.5 + - - -
131A THR* 6.5 0.4 - - - -
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 3.2 12.1 + - - +
32A LEU* 3.0 13.1 + - - +
34A GLY* 1.3 77.0 - - - +
36A GLY* 1.3 58.9 + - - +
37A LEU* 3.2 36.2 - - + +
131A THR* 3.7 19.5 + - + +
134A LEU* 4.1 8.9 - - - +
135A GLU* 3.3 50.1 + - + +
138A ILE* 4.1 3.6 - - - +
139A CYS* 4.5 7.1 - - - -
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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