Contacts of the helix formed by residues 34 - 52 (chain A) in PDB entry 2B9R
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 THR 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.0 17.9 - - - +
32A GLU 5.0 3.6 - - - +
33A VAL* 1.3 75.8 - - - +
35A GLY* 1.3 59.0 + - - +
36A ASN* 3.3 7.6 + - - +
37A MET* 3.0 39.9 + - + +
38A ARG 3.0 18.9 + - - -
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Residues in contact with GLY 35 (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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28A LEU* 3.7 6.1 - - - +
34A THR* 1.3 71.7 - - - +
36A ASN* 1.3 61.1 + - - +
37A MET 3.1 1.3 - - - -
38A ARG* 3.2 5.8 + - - +
39A ALA* 2.8 23.6 + - - +
168A LEU 5.2 0.2 - - - +
170A TYR* 3.5 40.8 - - - +
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Residues in contact with ASN 36 (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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34A THR* 3.3 6.3 + - - +
35A GLY* 1.3 73.1 - - - +
37A MET* 1.3 57.3 + - - +
39A ALA* 3.4 11.2 - - + -
40A ILE* 2.6 40.1 + - + +
233A HIS* 4.6 10.8 - - + +
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Residues in contact with MET 37 (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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32A GLU 5.0 1.3 - - - +
33A VAL* 3.7 8.1 - - + -
34A THR* 3.0 51.8 + - + +
35A GLY 3.1 0.2 - - - -
36A ASN* 1.3 76.9 - - - +
38A ARG* 1.3 57.6 + - - +
40A ILE* 2.5 44.0 - - + +
41A LEU 3.2 2.9 + - - -
77A LYS* 4.4 22.7 - - + -
80A LEU* 3.7 24.3 - - + +
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Residues in contact with ARG 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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27A TYR* 3.4 25.6 - - - +
28A LEU* 4.2 7.6 - - + -
33A VAL* 4.6 1.5 - - + +
34A THR 3.0 12.6 + - - +
35A GLY 3.2 8.3 + - - +
37A MET* 1.3 75.5 - - - +
39A ALA* 1.3 62.9 + - - +
41A LEU* 3.4 8.7 + - + +
42A ILE* 3.2 47.7 + - + +
63A VAL* 4.3 3.0 - - - +
66A ILE* 5.1 3.7 - - + +
67A ASP* 2.6 36.2 + - - -
70A MET* 4.3 14.4 - - + -
80A LEU* 4.3 5.8 - - - +
167A MET 2.8 27.7 + - - -
168A LEU 3.4 16.8 + - - -
169A ASP 4.0 10.1 + - - -
170A TYR* 4.2 19.0 - - - +
173A VAL* 4.4 8.1 - - - +
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Residues in contact with ALA 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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35A GLY 2.8 8.5 + - - +
36A ASN* 3.2 22.4 - - + +
37A MET 3.1 0.4 - - - -
38A ARG* 1.3 74.2 - - - +
40A ILE* 1.3 69.8 + - - +
41A LEU 2.9 1.2 + - - -
42A ILE* 3.1 5.8 + - - +
43A ASP* 3.0 20.6 + - - +
168A LEU* 4.4 23.8 - - + +
233A HIS* 4.1 19.7 - - + +
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Residues in contact with ILE 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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36A ASN* 2.6 21.5 + - + +
37A MET* 2.5 56.3 - - + +
39A ALA* 1.3 72.0 - - - +
41A LEU* 1.3 68.6 + - - +
43A ASP* 3.4 3.8 + - - +
44A TRP* 3.0 22.9 + - - +
80A LEU* 5.2 2.5 - - + -
233A HIS* 3.4 26.7 - - + -
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Residues in contact with LEU 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 MET 3.2 7.6 + - - +
38A ARG* 3.5 12.1 - - + +
39A ALA 2.9 1.6 + - - -
40A ILE* 1.3 82.1 - - + +
42A ILE* 1.3 60.3 + - + +
44A TRP* 2.8 21.3 + - + +
45A LEU* 2.7 56.7 + - + +
66A ILE* 4.0 14.6 - - + -
70A MET* 5.5 0.7 - - + -
80A LEU* 3.9 32.8 - - + +
81A GLN* 4.0 25.8 - - + +
83A VAL* 5.8 0.2 - - + -
84A GLY* 4.0 16.2 - - - +
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Residues in contact with ILE 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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38A ARG* 3.2 65.0 + - + +
39A ALA 3.1 4.2 + - - +
41A LEU* 1.3 80.3 - - + +
43A ASP* 1.3 63.8 + - - +
45A LEU* 3.1 8.6 + - + +
46A VAL* 2.9 22.3 + - - +
59A MET* 4.5 0.9 - - + -
63A VAL* 3.9 29.4 - - + -
66A ILE* 4.7 11.9 - - + -
167A MET* 3.4 22.2 - - + +
168A LEU* 3.6 20.6 - - + -
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Residues in contact with ASP 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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39A ALA 3.0 11.2 + - - +
40A ILE 3.4 10.2 - - - +
42A ILE* 1.3 76.1 - - - +
44A TRP* 1.3 65.7 + - - +
46A VAL* 3.0 17.5 + - - +
47A GLN* 3.2 27.4 + - - +
168A LEU* 3.6 13.2 - - + +
232A LYS 4.7 1.9 - - - +
233A HIS* 3.3 39.3 - - + +
234A MET 3.5 0.2 + - - -
235A THR* 2.4 35.8 + - - +
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Residues in contact with TRP 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 ILE 3.0 12.6 + - - +
41A LEU* 2.8 20.0 + - + +
43A ASP* 1.3 73.3 + - - +
45A LEU* 1.3 100.7 + - + +
47A GLN* 3.0 35.9 + - + +
48A VAL* 3.1 31.3 + - + +
51A LYS* 4.9 7.8 - - - +
81A GLN* 3.4 41.1 - - + +
85A VAL* 3.4 28.7 - - + -
108A VAL* 3.5 27.1 + - + -
109A THR* 4.2 5.6 - - + -
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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 LEU* 2.7 43.0 + - + +
42A ILE* 3.5 10.8 - - + +
44A TRP* 1.3 101.5 - - + +
46A VAL* 1.3 58.0 + - - +
48A VAL* 3.2 5.8 + - + +
49A GLN* 2.8 27.5 + - - +
59A MET* 4.1 9.2 - - + -
62A THR* 4.4 4.5 - - + -
63A VAL* 5.8 0.2 - - + -
66A ILE* 3.5 25.8 - - + -
84A GLY* 3.7 18.8 - - - +
85A VAL* 4.2 3.8 - - + +
88A MET* 3.7 28.6 - - + +
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Residues in contact with VAL 46 (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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42A ILE* 2.9 21.4 + - + +
43A ASP* 3.0 10.9 + - - +
45A LEU* 1.3 77.4 - - - +
47A GLN* 1.3 58.1 + - - +
49A GLN* 2.8 31.9 + - - +
50A MET* 3.0 28.8 + - + +
59A MET* 3.7 19.1 - - + -
164A GLU* 4.6 3.4 - - - +
167A MET* 3.8 18.2 - - + -
168A LEU* 5.3 0.4 - - + -
235A THR* 4.3 17.9 - - - +
236A VAL* 4.5 14.1 - - + -
239A LYS* 4.8 9.4 - - + +
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Residues in contact with GLN 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 ASP* 3.2 28.7 + - - +
44A TRP* 3.0 27.8 + - + +
46A VAL* 1.3 71.8 - - - +
48A VAL* 1.3 67.8 + - + +
50A MET* 3.1 17.5 + - + +
51A LYS* 2.9 37.5 + - + +
235A THR* 3.6 24.0 - - + +
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Residues in contact with VAL 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 TRP* 3.1 51.9 + - + +
45A LEU* 3.6 6.7 - - + +
47A GLN* 1.3 74.6 - - - +
49A GLN* 1.3 64.9 + - - +
50A MET 3.1 0.3 + - - -
51A LYS* 3.1 18.0 + - + +
52A PHE* 2.8 44.0 + - + +
85A VAL* 6.1 1.1 - - + -
88A MET* 4.1 17.9 - - - -
105A PHE* 4.8 3.6 - - + -
108A VAL* 4.2 21.1 - - + -
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Residues in contact with GLN 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 2.8 13.9 + - - +
46A VAL* 2.8 15.0 + - - +
48A VAL* 1.3 78.1 - - - +
50A MET* 1.3 59.8 + - - +
52A PHE 3.5 0.3 - - - -
53A ARG 2.9 5.2 + - - -
54A LEU* 2.5 76.8 + - + +
55A LEU 3.3 16.0 - - - -
56A GLN* 3.5 20.5 + - - +
58A THR* 6.1 0.2 - - + -
59A MET* 3.5 36.8 - - + +
88A MET* 4.4 3.8 - - - -
239A LYS* 3.9 9.8 + - - +
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Residues in contact with MET 50 (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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46A VAL* 3.0 15.4 + - + +
47A GLN* 3.1 28.4 + - + +
49A GLN* 1.3 85.3 - - - +
51A LYS* 1.3 66.3 + - - +
52A PHE 3.1 1.6 - - - -
53A ARG* 2.8 20.4 + - - +
54A LEU 5.7 0.2 - - - -
235A THR* 5.1 8.3 - - + +
239A LYS* 3.4 41.7 - - + +
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Residues in contact with LYS 51 (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 TRP* 4.9 7.9 - - - +
47A GLN* 2.9 31.3 + - + +
48A VAL* 3.4 27.5 - - + +
50A MET* 1.3 76.8 - - + +
52A PHE* 1.3 70.7 + - + +
53A ARG* 3.5 13.0 + - - +
108A VAL* 4.5 23.3 + - + +
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Residues in contact with PHE 52 (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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48A VAL* 2.8 24.0 + - + +
51A LYS* 1.3 85.1 - - + +
53A ARG* 1.3 79.7 + - - +
54A LEU* 3.2 24.6 + - + +
100A PRO* 3.7 21.1 - - + -
104A ASP* 3.6 32.1 - - + -
105A PHE* 3.9 29.8 - + - -
108A VAL* 3.1 36.6 - - + -
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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