Contacts of the helix formed by residues 36 - 46 (chain B) in PDB entry 1I7M
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 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 3.3 30.7 - - + +
34B THR 3.0 11.0 - - - +
35B ILE* 1.3 88.2 - - - +
37B ARG* 1.3 65.7 + - - +
38B SER* 4.1 11.9 - - - +
39B GLU* 3.0 34.3 + - + +
40B TRP* 3.4 5.9 + - - -
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE 3.8 0.6 + - - -
36B PRO* 1.3 72.0 - - - +
38B SER* 1.3 64.1 + - - +
40B TRP* 3.0 11.2 + - - +
41B ASP* 2.9 48.1 + - - +
51B ILE* 3.6 45.7 + - - +
54B VAL* 3.9 26.9 - - - +
63B TYR* 4.8 9.0 - - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 4.5 9.8 - - - +
37B ARG* 1.3 78.8 - - - +
39B GLU* 1.3 68.7 + - - +
41B ASP* 3.4 13.2 + - - +
42B ILE* 3.1 28.9 + - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.4 20.6 - - + +
101A TYR* 2.8 41.4 + - + +
35B ILE* 3.6 14.4 - - + -
36B PRO* 3.0 27.7 + - + +
38B SER* 1.3 78.4 - - - +
40B TRP* 1.3 60.1 + - - +
42B ILE* 3.1 23.0 + - - +
43B LEU* 2.9 29.7 + - - +
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Residues in contact with TRP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MSE 3.5 30.5 - - + +
72A VAL* 4.1 21.8 - - + +
77A PHE* 3.5 30.1 - + - -
94A LEU* 3.9 9.6 - - + -
97A LEU* 4.6 4.7 - - + -
32B LEU* 5.0 1.3 + - + -
33B ARG* 5.9 0.2 - - - +
35B ILE* 3.4 54.5 + - + +
36B PRO 3.4 13.9 + - - -
37B ARG* 3.0 13.9 + - - +
39B GLU* 1.3 76.6 - - - +
41B ASP* 1.3 63.7 + - - +
43B LEU* 3.4 29.8 + - + -
44B LEU* 3.0 32.7 + - + +
51B ILE* 4.0 10.5 - - + -
61B GLU* 4.9 2.2 + - - -
63B TYR* 3.8 23.5 + + - -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 2.9 53.9 + - - +
38B SER* 3.4 12.4 - - - +
40B TRP* 1.3 76.9 - - - +
42B ILE* 1.3 56.3 + - + +
44B LEU* 3.8 3.3 - - - +
45B LYS* 2.9 32.4 + - - +
49B CYS 5.1 0.5 - - - +
50B SER* 5.4 3.4 + - - +
51B ILE* 3.9 12.5 + - - +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 3.3 11.4 - - - +
39B GLU* 3.1 30.3 + - - +
41B ASP* 1.3 75.8 - - + +
43B LEU* 1.3 66.6 + - - +
45B LYS* 3.1 7.9 + - + +
46B ASP* 3.0 39.1 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MSE 5.1 0.9 - - - -
77A PHE* 5.4 1.1 - - + -
79A LEU* 4.6 9.2 - - + -
90A ALA* 4.0 28.9 - - + +
93A PRO* 4.3 9.0 - - + -
94A LEU* 3.9 28.0 - - + +
97A LEU* 3.7 26.7 - - + -
39B GLU 2.9 17.0 + - - +
40B TRP* 3.8 22.9 - - + +
42B ILE* 1.3 79.0 - - - +
44B LEU* 1.3 82.7 + - + +
46B ASP* 3.6 16.6 + - - +
47B VAL* 3.8 9.0 - - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MSE 4.1 13.2 - - - -
79A LEU* 4.3 24.2 - - + -
81A THR* 5.7 1.1 - - + -
40B TRP 3.0 20.5 + - - +
41B ASP* 4.1 2.7 - - - +
43B LEU* 1.3 91.2 - - + +
45B LYS* 1.3 62.8 + - - +
46B ASP 3.3 0.4 - - - -
47B VAL* 3.2 15.4 + - + +
49B CYS* 3.1 55.5 + - - +
50B SER* 4.6 1.8 - - - +
51B ILE* 3.6 33.7 - - + +
65B LEU* 3.8 14.6 - - + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP 2.9 20.7 + - - +
42B ILE* 3.5 7.4 - - + +
44B LEU* 1.3 72.9 - - - +
46B ASP* 1.3 65.4 + - - +
47B VAL 3.0 5.6 + - - -
48B GLN* 2.1 61.5 + - - +
49B CYS 3.8 9.4 + - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 5.5 5.1 - - - +
90A ALA* 6.4 0.2 - - + -
93A PRO* 6.0 3.4 - - + +
42B ILE* 3.0 32.1 + - - +
43B LEU* 3.8 10.1 - - - +
44B LEU 3.3 0.6 - - - -
45B LYS* 1.3 84.8 - - - +
47B VAL* 1.3 63.0 + - + +
48B GLN* 3.8 6.5 + - - +
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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