Contacts of the helix formed by residues 27 - 38 (chain M) in PDB entry 1I94
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 LYS 27 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16M ASP 5.2 0.9 - - - -
20M THR* 4.6 6.3 - - - -
26M GLY* 1.3 66.6 - - - +
28M ALA* 1.3 67.4 + - - +
29M ARG 3.6 0.4 - - - -
30M ALA* 3.4 15.9 - - - +
31M LYS* 2.9 24.8 + - - +
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Residues in contact with ALA 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309A C 3.2 51.8 - - - +
1310A A 3.5 4.0 - - - +
26M GLY 2.3 19.5 + - - +
27M LYS* 1.3 75.3 - - - +
29M ARG* 1.3 58.9 + - - +
31M LYS* 3.1 4.8 + - - +
32M GLU* 3.0 24.0 + - - +
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Residues in contact with ARG 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309A C 5.0 1.8 - - - +
1310A A 3.3 14.9 + - - +
24M GLY 4.7 4.9 - - - +
25M ILE* 4.6 15.0 - - + -
28M ALA* 1.3 76.5 - - - +
30M ALA* 1.3 57.8 + - - +
32M GLU* 3.7 10.2 - - + +
33M ALA* 2.6 35.0 + - - +
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Residues in contact with ALA 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M ASP* 2.8 39.5 - - + +
19M LEU* 4.7 14.8 - - + -
20M THR 5.0 3.4 - - - +
25M ILE* 5.1 1.3 - - - +
26M GLY 4.6 3.4 - - - +
27M LYS* 3.4 25.1 + - - +
28M ALA 3.1 0.2 - - - -
29M ARG* 1.3 80.5 - - - +
31M LYS* 1.3 66.7 + - - +
33M ALA* 3.1 10.6 + - - +
34M LEU* 3.2 13.2 + - - +
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Residues in contact with LYS 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M ASP* 5.0 6.2 - - - +
27M LYS 2.9 13.3 + - - +
28M ALA* 3.4 9.0 - - - +
30M ALA* 1.3 77.1 - - - +
32M GLU* 1.3 64.6 + - - +
33M ALA 2.7 2.3 + - - -
34M LEU* 2.9 4.8 + - - +
35M GLU* 2.7 23.5 + - + -
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Residues in contact with GLU 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ALA 3.0 13.4 + - - +
29M ARG* 3.8 10.3 - - - +
31M LYS* 1.3 78.0 - - - +
33M ALA* 1.3 63.1 + - - +
35M GLU* 3.2 10.8 - - - +
36M LYS* 3.2 21.5 + - - +
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Residues in contact with ALA 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU* 5.5 7.2 - - + -
29M ARG 2.6 22.5 + - - +
30M ALA* 3.2 8.5 - - - +
31M LYS 2.7 3.6 + - - -
32M GLU* 1.3 72.6 - - - +
34M LEU* 1.3 65.2 + - - +
36M LYS* 3.9 1.9 - - - +
37M THR* 3.0 28.1 + - - -
56M LEU* 6.3 2.9 - - + -
59M TYR* 6.0 3.2 - - + +
60M VAL* 5.5 13.2 - - + +
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M VAL* 6.1 2.2 - - + -
16M ASP* 5.5 5.8 - - + +
30M ALA 3.2 5.5 + - - +
31M LYS* 2.9 10.5 + - - +
33M ALA* 1.3 74.3 - - - +
35M GLU* 1.3 70.8 + - - +
37M THR* 4.3 6.5 - - - -
38M GLY* 2.7 20.3 + - - -
39M ILE* 3.4 26.6 + - + +
41M PRO* 4.5 17.7 - - + -
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Residues in contact with GLU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M LYS 2.7 17.8 + - - +
32M GLU* 3.2 18.6 - - - +
34M LEU* 1.3 76.5 - - - +
36M LYS* 1.3 67.1 + - - +
38M GLY* 3.1 6.2 + - - -
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Residues in contact with LYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLU 3.2 11.3 + - - +
33M ALA* 3.9 1.6 - - - +
35M GLU* 1.3 78.5 - - - +
37M THR* 1.3 55.2 + - - +
38M GLY* 2.5 20.0 + - - -
59M TYR* 6.2 3.4 - - + -
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Residues in contact with THR 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ALA* 3.0 19.6 + - - -
34M LEU* 4.3 4.3 - - - -
36M LYS* 1.3 75.4 - - - +
38M GLY* 1.3 66.2 + - - +
39M ILE* 4.7 6.4 - - - +
52M GLU 5.8 0.7 - - - -
55M ARG* 5.0 12.3 - - - +
56M LEU* 4.9 22.7 - - - -
59M TYR* 5.4 8.8 - - - +
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Residues in contact with GLY 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LEU 2.7 16.5 + - - -
35M GLU 3.5 4.7 - - - -
36M LYS 2.5 13.0 + - - -
37M THR* 1.3 75.5 - - - +
39M ILE* 1.3 57.0 + - - +
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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