Contacts of the helix formed by residues 32 - 43 (chain A) in PDB entry 2CPW
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 PRO 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 0.7 - - + -
30A GLY 4.3 3.4 - - - +
31A PHE* 1.4 89.5 - - + +
33A ARG* 1.3 69.5 + - - +
34A ALA* 4.2 8.5 - - + +
35A ARG* 2.8 46.2 + - + +
36A ALA 3.0 9.5 + - - -
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Residues in contact with ARG 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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23A LEU* 3.8 25.6 - - + -
27A LEU* 3.0 29.8 - - + +
32A PRO* 1.3 70.6 - - - +
34A ALA* 1.3 52.2 + - - +
36A ALA* 3.3 1.6 + - - +
37A GLN* 2.5 60.9 + - + +
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Residues in contact with ALA 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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32A PRO* 2.8 8.2 + - + -
33A ARG* 1.3 78.6 - - - +
35A ARG* 1.3 62.5 + - - +
37A GLN* 2.7 9.5 + - - +
38A LYS* 2.6 37.9 + - - +
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Residues in contact with ARG 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 PHE* 4.7 5.4 - - + -
32A PRO* 2.8 39.6 + - + +
34A ALA* 1.3 81.4 - - - +
36A ALA* 1.3 62.6 + - - +
38A LYS* 3.4 6.1 + - - +
39A ALA* 2.9 24.6 + - - +
54A TRP* 4.3 0.3 - - - -
55A LEU* 3.2 30.6 - - + +
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Residues in contact with ALA 36 (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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23A LEU* 3.5 26.7 - - + -
26A LEU* 3.4 39.9 - - + -
27A LEU* 5.1 0.4 - - + -
31A PHE* 5.1 1.3 - - + +
32A PRO 3.0 7.7 + - - +
33A ARG* 3.6 1.6 - - - +
35A ARG* 1.3 78.2 - - - +
37A GLN* 1.3 54.2 - - - +
39A ALA* 3.5 3.6 - - - +
40A LEU* 2.5 44.0 + - + +
55A LEU* 4.6 3.1 - - - +
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Residues in contact with GLN 37 (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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23A LEU* 4.3 17.8 - - + +
33A ARG* 2.5 47.5 + - + +
34A ALA* 2.7 11.1 + - - +
36A ALA* 1.3 67.2 - - - +
38A LYS* 1.3 59.8 + - - +
40A LEU* 3.0 8.0 + - + +
41A ALA* 2.6 40.6 + - - +
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Residues in contact with LYS 38 (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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34A ALA 2.6 18.8 + - - +
35A ARG* 3.7 5.6 - - - +
37A GLN* 1.3 72.7 - - - +
39A ALA* 1.3 62.7 + - - +
41A ALA* 3.5 10.2 + - - +
42A SER* 2.9 33.7 + - - +
54A TRP* 3.4 22.4 - - + -
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Residues in contact with ALA 39 (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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35A ARG 2.9 15.5 + - - +
36A ALA 3.5 3.1 - - - +
38A LYS* 1.3 73.1 - - - +
40A LEU* 1.3 70.1 + - - +
42A SER* 2.9 5.4 + - - -
43A THR* 2.7 27.3 + - - +
51A ALA* 3.8 17.3 - - + +
54A TRP* 3.1 34.7 - - + -
55A LEU* 3.7 14.8 - - + -
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Residues in contact with LEU 40 (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 ALA* 3.8 26.5 - - + +
23A LEU* 3.5 37.0 - - + +
26A LEU* 4.4 7.9 - - + -
36A ALA* 2.5 38.3 + - + +
37A GLN* 3.5 7.0 - - + +
39A ALA* 1.3 71.2 - - - +
41A ALA* 1.3 52.4 + - - +
43A THR* 2.8 9.1 - - - +
44A GLY 2.5 45.7 + - - +
45A GLY* 3.6 21.1 - - - -
47A SER 4.8 8.5 - - - +
48A VAL* 5.3 0.4 - - + -
51A ALA* 4.3 3.8 - - + +
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Residues in contact with ALA 41 (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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37A GLN* 2.6 23.8 + - - +
38A LYS* 3.6 12.8 - - - +
40A LEU* 1.3 70.4 - - - +
42A SER* 1.3 58.8 + - - +
44A GLY* 2.5 31.3 + - - -
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Residues in contact with SER 42 (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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38A LYS* 2.9 25.3 + - - +
39A ALA 2.9 7.8 + - - -
41A ALA* 1.3 74.2 - - - +
43A THR* 1.3 58.9 + - - +
44A GLY 3.2 2.1 + - - -
54A TRP* 3.3 39.3 + - - -
59A SER* 5.2 0.2 + - - -
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Residues in contact with THR 43 (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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39A ALA 2.7 22.1 + - - +
40A LEU* 2.8 9.3 + - - +
42A SER* 1.3 72.3 - - - +
44A GLY* 1.3 49.2 + - - +
45A GLY* 2.6 18.7 + - - -
46A ARG* 3.9 8.3 + - - +
47A SER 5.1 2.6 + - - -
50A THR* 3.9 29.6 - - + +
51A ALA* 4.0 9.9 - - - +
54A TRP* 4.1 28.3 - - + -
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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