Contacts of the helix formed by residues 34 - 42 (chain A) in PDB entry 4CBS
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASN 3.8 1.6 - - - +
33A LEU* 1.3 89.5 - - + +
35A PRO* 1.3 78.5 - - + +
36A ARG* 4.5 2.2 - - + +
37A ILE* 3.2 25.3 + - + -
38A MET* 3.2 18.6 + - - +
212A ASN* 3.7 25.8 - - + +
278A LEU* 4.0 16.2 - - + -
366A CYS* 3.9 23.5 - - + -
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Residues in contact with PRO 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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33A LEU 4.8 0.2 - - - +
34A PRO* 1.3 88.7 - - + +
36A ARG* 1.3 57.3 + - - +
38A MET* 3.3 13.5 + - + +
39A ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 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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34A PRO* 3.3 1.6 - - + +
35A PRO* 1.3 80.8 - - - +
37A ILE* 1.3 59.3 + - + +
39A ALA* 3.2 8.8 + - + +
40A ALA* 3.0 28.4 + - - +
273A ARG* 3.8 5.7 - - - +
274A GLU* 2.7 47.3 + - + +
277A ALA* 3.5 18.5 - - - +
278A LEU* 3.6 38.8 - - + +
281A GLU* 3.1 27.5 + - - -
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Residues in contact with ILE 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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33A LEU* 4.3 6.5 - - + -
34A PRO* 3.2 27.7 + - + +
36A ARG* 1.3 74.6 - - - +
38A MET* 1.3 65.2 + - - +
40A ALA* 3.4 6.1 + - - +
41A GLY* 3.0 18.0 + - - -
211A LEU 3.8 3.4 - - - +
212A ASN 3.2 30.1 - - - +
213A ALA* 4.1 0.4 - - - -
214A PRO* 3.9 25.0 - - + +
271A SER* 3.5 16.1 + - - +
274A GLU* 4.4 3.8 - - + -
275A SER* 3.6 39.3 - - - +
278A LEU* 4.0 11.9 - - + -
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Residues in contact with MET 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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33A LEU* 3.8 39.3 - - + +
34A PRO 3.2 15.6 + - - +
35A PRO* 3.3 11.4 + - + +
37A ILE* 1.3 75.8 - - - +
39A ALA* 1.3 62.5 + - - +
41A GLY* 3.0 12.0 + - - +
42A GLY* 3.2 10.2 + - - -
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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 PRO 2.9 14.5 + - - +
36A ARG* 3.4 13.0 - - + +
38A MET* 1.3 74.5 - - - +
40A ALA* 1.3 66.4 + - - +
42A GLY* 3.1 13.0 + - - -
43A LEU* 3.5 15.0 + - - +
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Residues in contact with ALA 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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36A ARG 3.0 12.5 + - - +
37A ILE 3.6 8.5 - - - +
39A ALA* 1.3 75.5 - - - +
41A GLY* 1.3 62.5 - - - +
42A GLY 3.2 1.0 + - - -
43A LEU* 3.3 31.5 + - + +
267A ILE* 4.4 0.7 - - - +
270A TYR* 3.6 16.5 - - + +
271A SER* 3.9 19.7 - - - +
274A GLU* 3.7 24.5 - - + -
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Residues in contact with GLY 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 ILE 3.0 11.7 + - - -
38A MET* 3.0 8.0 + - - -
40A ALA* 1.3 77.8 - - - +
42A GLY* 1.3 57.1 + - - +
43A LEU 3.3 1.3 + - - +
267A ILE* 3.5 22.7 - - - +
271A SER* 3.7 13.0 - - - -
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Residues in contact with GLY 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 MET 3.2 6.4 + - - -
39A ALA 3.1 11.0 + - - -
41A GLY* 1.3 77.6 - - - +
43A LEU* 1.3 61.8 + - - +
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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