Contacts of the helix formed by residues 37 - 49 (chain C) in PDB entry 2H1O
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 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C LEU 3.8 0.8 + - - -
36C SER* 1.3 71.2 + - - +
38C ILE* 1.3 52.1 + - + +
40C VAL* 3.2 5.8 + - - +
41C ALA* 2.8 29.5 + - - +
75C ILE* 3.9 12.8 - - + +
76C LEU 2.5 20.8 + - - +
77C PRO* 4.0 1.3 - - + -
78C PHE 4.8 0.9 - - - +
78D PHE* 3.4 31.6 - - + +
79D ASP* 3.7 22.4 - - - -
80D GLU 3.9 2.2 - - - +
83D ALA* 3.5 7.8 - - - +
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Residues in contact with ILE 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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36C SER* 2.8 14.5 + - - +
37C ALA* 1.3 73.4 - - - +
39C THR* 1.3 65.5 + - - +
41C ALA* 2.8 15.9 + - - +
42C GLU* 2.9 25.8 + - + +
78C PHE* 4.8 12.3 - - + -
103C ALA* 4.9 3.1 - - + +
106C TYR* 4.0 38.6 - - + -
107C ILE* 3.3 23.1 - - + -
110C THR* 5.8 0.2 - - - +
38D ILE* 4.9 2.7 - - + -
78D PHE* 3.5 32.1 - - + -
106D TYR* 4.2 22.7 - - + +
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Residues in contact with THR 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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4C LEU 3.9 13.2 + - - +
5C ASP* 3.5 22.3 + - - +
6C THR* 3.6 31.8 + - - +
9C ILE* 4.8 0.2 - - + -
35C LEU* 4.4 9.4 - - + -
36C SER* 2.8 22.9 + - - -
38C ILE* 1.3 77.0 - - - +
40C VAL* 1.3 61.7 + - - +
42C GLU* 3.2 5.0 + - - +
43C MET* 2.9 37.1 + - - +
107C ILE* 4.1 7.1 - - - +
68G ARG* 4.1 1.9 + - - -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.2 14.6 - - + -
36C SER 3.0 11.5 + - - +
37C ALA* 3.5 9.2 - - - +
39C THR* 1.3 73.7 - - - +
41C ALA* 1.3 69.2 + - - +
43C MET* 3.8 7.8 - - + +
44C ARG* 3.1 54.5 + - + +
68C LEU* 4.0 27.6 - - + -
75C ILE* 3.6 29.8 - - + -
80D GLU* 4.9 6.1 - - + -
83D ALA* 4.3 3.8 - - + -
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Residues in contact with ALA 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 ALA 2.8 13.3 + - - +
38C ILE* 2.8 12.0 + - + +
40C VAL* 1.3 78.6 - - - +
42C GLU* 1.3 64.2 + - + +
44C ARG* 3.1 3.3 + - - +
45C LEU* 3.0 20.6 + - - +
78D PHE* 4.0 11.7 - - + -
83D ALA* 3.8 22.2 - - + +
86D TYR* 3.7 28.0 - - + -
87D ALA* 4.3 2.3 - - - +
106D TYR* 5.0 3.1 - - + +
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Residues in contact with GLU 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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6C THR* 2.4 40.5 + - + +
38C ILE* 2.9 25.8 + - + +
39C THR* 3.4 7.0 - - - +
41C ALA* 1.3 77.5 - - + +
43C MET* 1.3 54.2 + - - +
45C LEU* 2.9 10.0 + - - +
46C GLY* 2.7 34.0 + - - -
103C ALA* 4.7 1.7 - - - +
86D TYR* 4.9 4.9 - - + +
106D TYR* 5.5 3.3 + - - +
66G ASP 5.2 1.8 - - - +
67G VAL* 4.0 25.1 - - + +
68G ARG* 2.6 39.7 + - - +
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Residues in contact with MET 43 (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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6C THR* 4.3 16.6 - - + +
9C ILE* 3.6 44.0 - - + -
10C SER* 5.2 3.1 - - - +
13C LEU* 6.2 2.9 - - + -
35C LEU* 4.5 6.1 - - + -
39C THR* 2.9 31.1 + - - +
40C VAL* 3.8 7.0 - - + +
42C GLU* 1.3 72.6 - - - +
44C ARG* 1.3 63.9 + - + +
46C GLY* 3.4 2.1 + - - -
47C VAL* 3.1 29.1 + - - +
63C MET* 3.4 40.2 - - + -
67C ILE* 4.4 4.3 - - + -
68C LEU* 4.3 11.4 - - + -
64G LEU* 4.5 12.0 - - + +
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Residues in contact with ARG 44 (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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40C VAL* 3.1 30.6 + - + +
41C ALA 3.5 7.2 - - - +
43C MET* 1.3 78.4 - - + +
45C LEU* 1.3 58.6 + - - +
47C VAL* 3.4 8.0 + - - +
48C ALA* 2.9 28.9 + - - +
60C HIS* 6.4 0.2 - - + -
63C MET* 5.6 3.8 - - + -
64C GLU* 2.7 42.4 + - - +
68C LEU* 3.2 24.3 - - + +
80D GLU* 2.7 43.6 + - - +
83D ALA 4.5 0.9 - - - -
84D ALA* 3.6 30.2 - - - +
87D ALA* 3.5 14.2 - - + +
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Residues in contact with LEU 45 (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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41C ALA 3.0 11.8 + - - +
42C GLU* 2.9 9.7 + - - +
44C ARG* 1.3 73.0 - - - +
46C GLY* 1.3 67.1 + - - +
47C VAL 3.1 0.2 - - - -
48C ALA* 4.2 1.3 - - - -
49C LEU* 3.0 46.2 + - + +
86D TYR* 3.9 28.0 - - + +
87D ALA* 3.8 13.0 - - + +
90D ARG* 3.9 21.1 - - + +
91D SER* 3.8 27.4 - - - +
94D LYS* 5.1 2.0 - - - +
67G VAL* 3.7 29.2 - - + -
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Residues in contact with GLY 46 (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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42C GLU 2.7 19.5 + - - -
43C MET 3.8 2.5 - - - -
45C LEU* 1.3 75.4 - - - +
47C VAL* 1.3 61.3 + - - +
49C LEU* 3.8 5.7 + - - -
50C LEU* 3.9 2.4 - - - +
64G LEU* 3.7 21.3 - - - +
65G GLU* 2.8 37.3 - - - +
67G VAL* 5.4 3.1 - - - +
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Residues in contact with VAL 47 (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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43C MET 3.1 15.0 + - - +
44C ARG* 3.5 10.1 - - - +
45C LEU 3.1 0.2 - - - -
46C GLY* 1.3 76.0 - - - +
48C ALA* 1.3 68.0 + - - +
50C LEU* 3.1 32.2 + - + +
56C LYS* 3.8 14.3 - - + +
59C LEU* 4.1 17.3 - - + -
60C HIS* 4.4 35.2 - - + +
63C MET* 4.1 24.9 - - + -
64G LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 48 (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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44C ARG 2.9 17.9 + - - +
45C LEU* 3.8 3.8 - - - +
47C VAL* 1.3 77.8 - - - +
49C LEU* 1.3 56.0 + - - +
50C LEU 3.2 1.5 + - - +
56C LYS* 3.0 29.6 + - - +
87D ALA* 4.1 7.9 - - + +
88D GLN* 5.7 0.2 - - - -
91D SER* 3.3 34.1 - - - +
95D THR* 5.0 4.0 - - - +
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Residues in contact with LEU 49 (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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45C LEU* 3.0 31.4 + - + +
46C GLY 4.2 5.2 - - - +
47C VAL 3.1 0.8 + - - -
48C ALA* 1.3 72.4 - - - +
50C LEU* 1.3 65.5 + - - +
51C LEU* 4.4 6.1 - - - +
91D SER* 4.0 19.1 - - - -
94D LYS* 4.2 27.4 - - + -
95D THR* 4.0 28.7 - - + +
65G GLU* 4.2 25.5 - - + +
67G VAL* 4.1 25.1 - - + -
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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