Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 2H1C
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU 3.9 0.8 + - - -
36A SER* 1.3 73.2 + - - +
38A ILE* 1.3 58.1 + - + +
40A VAL* 3.4 5.3 + - - +
41A ALA* 3.0 27.5 + - - +
75A ILE* 3.9 18.8 - - + +
76A LEU 2.8 19.2 + - - +
77A PRO* 4.2 12.6 - - + -
78A PHE* 4.9 3.6 - - + +
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Residues in contact with ILE 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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36A SER* 2.9 15.3 + - - +
37A ALA* 1.3 79.3 - - + +
39A THR* 1.3 57.2 + - - +
41A ALA* 3.3 8.6 + - + +
42A GLU* 3.0 50.5 + - + +
78A PHE* 4.7 13.9 - - + -
103A ALA* 4.8 4.9 - - + +
106A TYR* 3.9 42.4 - - + -
107A ILE* 4.6 13.2 - - + -
205A MG 4.3 6.1 - - - -
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Residues in contact with THR 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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4A LEU 4.0 6.0 + - - +
5A ASP 4.2 0.2 - - - -
6A THR* 3.2 40.9 + - - +
9A ILE* 4.4 3.8 - - + -
35A LEU* 4.5 6.5 - - + -
36A SER* 3.0 7.9 + - - -
38A ILE* 1.3 75.2 - - - +
40A VAL* 1.3 61.5 + - - +
42A GLU* 3.2 4.3 + - - +
43A LEU* 2.8 47.1 + - + +
107A ILE* 3.9 16.3 - - - +
203A MG 2.7 27.6 - - - -
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Residues in contact with VAL 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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35A LEU* 4.1 24.7 - - + -
36A SER 3.1 13.9 + - - +
37A ALA* 3.6 8.7 - - - +
38A ILE 3.3 0.2 - - - -
39A THR* 1.3 74.4 - - - +
41A ALA* 1.3 59.3 + - - +
43A LEU* 3.3 8.2 + - + +
44A ARG* 2.9 64.4 + - + +
68A LEU* 4.0 16.8 - - + -
75A ILE* 3.8 30.3 - - + -
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Residues in contact with ALA 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 ALA 3.0 14.0 + - - +
38A ILE* 3.4 13.2 - - + +
39A THR 3.2 0.2 - - - -
40A VAL* 1.3 78.6 - - - +
42A GLU* 1.3 58.5 + - + +
44A ARG* 3.4 8.4 + - - +
45A LEU* 2.9 29.9 + - - +
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Residues in contact with GLU 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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6A THR* 2.6 38.3 + - + +
38A ILE* 3.0 32.2 + - + +
39A THR* 3.2 6.2 + - - +
41A ALA* 1.3 74.5 - - + +
43A LEU* 1.3 61.7 + - - +
45A LEU* 3.4 8.8 + - + +
46A GLY* 2.9 26.2 + - - -
103A ALA* 4.3 17.2 - - - +
107A ILE* 4.9 5.9 - - - +
64B LEU* 5.7 1.6 - - - +
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Residues in contact with LEU 43 (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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6A THR* 3.9 11.4 - - + -
9A ILE* 3.8 37.7 - - + -
10A SER* 3.4 25.8 - - - +
13A LEU* 5.7 2.0 - - + -
35A LEU* 5.0 6.1 - - + -
39A THR* 2.8 31.2 + - + +
40A VAL* 3.7 9.0 - - + +
42A GLU* 1.3 76.3 - - - +
44A ARG* 1.3 63.6 + - - +
46A GLY* 3.3 2.5 + - - -
47A VAL* 3.1 27.5 + - - +
63A LEU* 4.3 22.9 - - + -
68A LEU* 5.4 2.5 - - + -
64B LEU* 4.4 17.9 - - + +
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Residues in contact with ARG 44 (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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40A VAL* 2.9 36.1 + - + +
41A ALA* 3.8 6.5 - - - +
43A LEU* 1.3 77.6 - - - +
45A LEU* 1.3 60.8 + - - +
47A VAL* 3.5 0.9 + - - -
48A ALA* 3.0 13.0 + - - +
63A LEU* 3.8 13.5 - - + -
64A GLU* 2.9 42.9 + - - +
68A LEU* 3.2 18.6 - - - +
75A ILE* 6.1 0.6 - - - +
204A MG 2.6 27.9 - - - -
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Residues in contact with LEU 45 (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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41A ALA 2.9 18.8 + - - +
42A GLU* 3.7 8.5 - - + +
43A LEU 3.2 0.2 - - - -
44A ARG* 1.3 72.3 - - - +
46A GLY* 1.3 67.8 + - - +
48A ALA* 3.1 9.4 + - + +
49A LEU* 3.0 56.3 + - + +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU 2.9 14.7 + - - -
43A LEU 3.3 3.8 + - - -
45A LEU* 1.3 78.6 - - - +
47A VAL* 1.3 62.1 + - - +
49A LEU* 3.2 17.2 + - - +
50A LEU* 3.5 13.5 + - - +
63B GLU 5.9 0.4 - - - -
64B LEU* 3.6 20.5 - - - +
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Residues in contact with VAL 47 (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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43A LEU 3.1 15.4 + - - +
44A ARG* 3.8 6.7 - - - +
46A GLY* 1.3 75.3 - - - +
48A ALA* 1.3 63.2 + - - +
49A LEU 3.2 1.2 + - - -
50A LEU* 3.2 20.7 + - + +
56A LYS* 3.3 23.3 - - + +
59A LEU* 3.7 30.7 - - + -
60A HIS* 3.8 33.2 - - + +
63A LEU* 4.1 16.6 - - + -
204A MG 4.0 6.1 - - - -
64B LEU* 3.7 10.7 - - + +
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Residues in contact with ALA 48 (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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44A ARG 3.0 18.1 + - - +
45A LEU* 3.1 10.9 + - + +
47A VAL* 1.3 77.7 - - - +
49A LEU* 1.3 62.1 + - + +
50A LEU 3.4 1.4 + - - +
56A LYS* 3.8 23.0 + - - +
204A MG 3.9 8.1 - - - -
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Residues in contact with LEU 49 (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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45A LEU* 3.0 48.5 + - + +
46A GLY* 3.2 8.3 + - - +
47A VAL 3.1 0.6 - - - -
48A ALA* 1.3 80.9 - - + +
50A LEU* 1.3 67.2 + - - +
51A LEU* 3.4 11.4 + - - +
140A ACT 4.7 0.5 - - - +
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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