Contacts of the helix formed by residues 33 - 42 (chain C) in PDB entry 1IVH
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 ALA 33 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU 2.9 11.9 + - - +
29C GLN* 3.5 18.4 - - + +
32C LEU* 1.3 75.4 - - - +
34C PRO* 1.3 69.9 - - + +
36C ALA* 3.2 18.2 + - - +
37C GLN 4.7 0.3 + - - -
89C ALA* 4.1 23.0 - - + +
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Residues in contact with PRO 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN 3.2 21.1 - - - +
30C GLU* 3.4 23.3 - - - +
31C HIS 4.7 1.6 - - - -
32C LEU 3.5 2.5 - - - +
33C ALA* 1.3 90.5 - - + +
35C LYS* 1.3 65.4 + - - +
36C ALA 3.6 0.2 + - - -
37C GLN* 4.4 9.0 + - - +
38C GLU* 5.1 1.4 + - - +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU 5.0 1.7 + - - -
31C HIS* 3.0 36.3 + - - +
32C LEU* 3.0 8.1 + - + +
34C PRO* 1.3 85.6 - - - +
36C ALA* 1.3 66.0 + - - +
37C GLN 3.3 1.1 - - - -
38C GLU* 3.0 15.1 + - + +
39C ILE* 2.9 36.2 + - + +
45C PHE* 5.0 4.5 - - + -
47C ASN* 3.7 34.9 - - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.1 7.7 + - - +
33C ALA 3.2 16.5 + - - +
35C LYS* 1.3 75.9 - - - +
37C GLN* 1.3 63.1 + - - +
39C ILE* 3.2 11.6 + - - +
40C ASP* 3.1 24.1 + - - +
89C ALA 3.3 23.3 - - - +
90C SER* 4.3 9.6 + - - +
363C ARG* 3.7 21.6 + - - +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA 4.7 0.6 + - - -
34C PRO 4.4 7.3 + - - +
35C LYS 3.3 0.6 - - - -
36C ALA* 1.3 79.0 - - - +
38C GLU* 1.3 63.7 + - - +
40C ASP* 3.4 5.2 + - - +
41C ARG* 2.9 55.1 + - + +
357C ASN 3.4 22.2 - - - +
358C ASP* 3.9 16.0 + - - +
363C ARG* 4.4 14.4 - - - +
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO 5.1 1.5 + - - +
35C LYS* 3.0 19.1 + - + +
37C GLN* 1.3 78.5 - - - +
39C ILE* 1.3 52.2 - - + +
41C ARG* 2.6 36.5 + - - +
42C SER* 2.6 58.0 + - - +
46C LYS* 5.4 9.9 - - + -
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.8 25.4 - - + -
35C LYS* 2.9 28.2 + - + +
36C ALA* 3.5 9.0 - - - +
38C GLU* 1.3 76.0 - - + +
40C ASP* 1.3 52.6 + - - +
43C ASN* 2.7 31.9 + - - -
44C GLU 3.1 23.9 + - - +
45C PHE* 3.6 35.2 - - + -
46C LYS 5.5 0.4 - - - +
90C SER* 4.5 4.5 - - - +
92C ALA* 4.5 7.4 - - + -
93C VAL* 4.1 8.1 - - + -
217C ARG 3.6 14.5 - - - +
218C GLY* 3.6 15.3 - - - -
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 3.1 7.9 + - - +
37C GLN* 3.7 3.8 - - - +
39C ILE* 1.3 79.5 - - - +
41C ARG* 1.3 63.6 + - - +
43C ASN 3.0 6.9 + - - -
217C ARG* 2.9 54.6 + - - +
363C ARG* 3.6 28.8 - - - +
366C ARG* 2.8 42.5 + - - -
367C ASP* 4.5 2.9 - - - +
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLN* 2.9 56.7 + - + +
38C GLU* 2.6 46.6 + - - +
40C ASP* 1.3 81.8 + - - +
42C SER* 1.3 61.2 + - - +
43C ASN 3.4 0.3 + - - -
217C ARG* 3.8 12.8 + - - +
357C ASN 5.3 1.0 + - - -
358C ASP* 5.9 0.8 + - - -
212D ASP* 5.6 4.4 + - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLU* 2.6 44.6 + - - +
41C ARG* 1.3 72.8 - - - +
43C ASN* 1.3 70.6 + - - +
44C GLU* 3.2 25.8 + - - +
46C LYS* 4.1 24.0 - - - -
217C ARG* 4.7 0.2 - - - -
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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