Contacts of the helix formed by residues 29 - 50 (chain A) in PDB entry 2DOS
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 SER 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN* 3.8 3.1 - - - -
28A PHE* 1.3 78.7 - - - +
30A PRO* 1.3 73.9 - - - +
31A VAL* 3.4 9.3 - - - +
32A GLU* 3.7 25.1 - - - +
33A LEU* 3.2 27.7 + - - +
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Residues in contact with PRO 30 (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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16A GLN* 3.2 41.0 - - + +
29A SER* 1.3 90.7 - - - +
31A VAL* 1.3 64.4 + - + +
33A LEU* 3.6 2.3 + - + +
34A SER* 2.9 30.5 + - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.1 10.3 - - - +
30A PRO* 1.3 82.2 - - + +
32A GLU* 1.3 86.2 + - + +
34A SER* 3.4 6.1 + - - -
35A SER* 3.0 25.2 + - - -
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Residues in contact with GLU 32 (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 PHE* 4.7 9.6 - - + -
29A SER* 3.6 25.1 + - - +
30A PRO 3.3 0.4 - - - -
31A VAL* 1.3 89.1 - - + +
33A LEU* 1.3 60.5 + - - +
35A SER* 3.3 8.5 + - - -
36A ILE* 2.9 39.5 + - + +
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Residues in contact with LEU 33 (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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15A ALA* 3.3 41.1 - - + +
16A GLN* 3.3 12.6 - - + +
19A LEU* 3.6 23.8 - - + -
28A PHE* 3.5 33.7 - - + -
29A SER 3.2 9.3 + - - +
30A PRO* 4.0 4.0 - - + +
32A GLU* 1.3 79.2 - - - +
34A SER* 1.3 63.1 + - - +
36A ILE* 3.3 9.7 + - + +
37A ALA 3.0 18.7 + - - -
75A PHE* 3.1 33.3 - - + -
79A VAL* 4.6 5.2 - - + -
83A ALA* 5.1 4.3 - - + -
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Residues in contact with SER 34 (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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30A PRO 2.9 20.4 + - - -
31A VAL* 3.6 7.6 + - - +
33A LEU* 1.3 78.3 - - - +
35A SER* 1.3 61.7 + - - +
37A ALA* 3.4 2.7 + - - +
38A HIS* 3.0 29.9 + - - +
75A PHE* 4.2 7.6 - - - -
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Residues in contact with SER 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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31A VAL* 3.0 18.6 + - - -
32A GLU* 3.3 10.0 + - - -
34A SER* 1.3 75.5 - - - +
36A ILE* 1.3 73.0 + - - +
38A HIS* 3.3 7.5 + - - +
39A GLN* 3.0 37.5 + - - +
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Residues in contact with ILE 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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28A PHE* 4.1 14.1 - - + -
32A GLU* 2.9 30.4 + - + +
33A LEU* 3.6 20.2 - - + +
35A SER* 1.3 85.7 + - - +
37A ALA* 1.3 57.6 + - - +
39A GLN* 3.4 13.1 + - - +
40A LEU* 3.0 38.2 + - + +
79A VAL* 3.8 16.8 - - + -
82A ASN* 5.9 5.4 - - + +
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Residues in contact with ALA 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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33A LEU 3.0 7.9 + - - +
34A SER* 3.8 4.0 - - - +
36A ILE* 1.3 74.9 - - - +
38A HIS* 1.3 60.0 + - - +
40A LEU* 3.2 0.9 + - - +
41A ASP* 2.8 43.4 + - - +
74A PHE 4.9 1.6 - - - +
75A PHE* 3.2 42.4 - - + -
79A VAL* 3.6 20.4 - - + +
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Residues in contact with HIS 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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34A SER* 3.0 22.3 + - - +
35A SER* 3.3 8.0 + - - +
37A ALA* 1.3 75.7 - - - +
39A GLN* 1.3 58.6 + - + +
41A ASP* 3.9 7.1 + - - +
42A GLU* 3.0 55.8 + - + +
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Residues in contact with GLN 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 SER* 3.0 31.0 + - - +
36A ILE* 3.7 14.5 - - - +
38A HIS* 1.3 74.8 - - + +
40A LEU* 1.3 55.1 + - + +
42A GLU* 3.7 4.6 - - - +
43A GLU* 2.8 39.0 + - - +
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Residues in contact with LEU 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 ILE* 3.0 28.0 + - + +
37A ALA 3.6 4.7 - - - +
39A GLN* 1.3 77.1 - - - +
41A ASP* 1.3 59.7 + - - +
43A GLU* 4.6 4.0 - - - +
44A GLU* 2.8 68.4 + - - +
78A GLN* 4.3 13.2 - - + +
79A VAL* 3.6 39.0 - - + +
82A ASN* 5.2 7.0 - - + -
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Residues in contact with ASP 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* 2.8 28.8 + - - +
38A HIS* 3.9 6.8 + - - +
40A LEU* 1.3 81.3 - - - +
42A GLU* 1.3 57.7 + - + +
44A GLU* 3.4 5.5 + - - +
45A ARG* 2.8 37.2 + - + +
65A PRO* 6.0 0.2 - - - -
66A SER* 4.7 20.8 + - - +
74A PHE 3.9 17.2 - - - +
75A PHE 5.8 0.2 - - - -
76A SER* 3.9 23.4 + - - -
78A GLN* 4.3 3.7 + - - +
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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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38A HIS* 3.0 40.8 + - + +
39A GLN* 3.7 5.4 - - - +
41A ASP* 1.3 77.6 - - + +
43A GLU* 1.3 62.7 + - - +
45A ARG* 3.1 9.7 + - - +
46A MET* 3.0 42.3 + - + +
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Residues in contact with GLU 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 GLN 2.8 22.6 + - - +
40A LEU* 3.9 6.1 - - - +
42A GLU* 1.3 73.6 - - - +
44A GLU* 1.3 68.3 + - - +
46A MET* 2.9 35.3 - - - +
47A ARG* 3.0 25.9 + - + +
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Residues in contact with GLU 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 LEU* 2.8 60.8 + - - +
41A ASP* 3.7 4.0 - - - +
43A GLU* 1.3 88.7 - - - +
45A ARG* 1.3 59.9 + - + +
47A ARG* 3.7 8.9 - - - -
48A MET* 2.8 44.9 + - - +
60A THR* 3.6 29.8 - - + -
65A PRO* 4.3 13.7 - - + -
78A GLN* 3.7 21.1 + - - +
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Residues in contact with ARG 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 ASP* 2.8 27.4 + - + +
42A GLU* 3.1 12.5 + - - +
44A GLU* 1.3 78.8 - - + +
46A MET* 1.3 57.2 + - - +
48A MET* 3.8 9.8 - - - +
49A ALA* 3.0 31.4 + - - +
66A SER* 4.1 26.1 + - - +
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Residues in contact with MET 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* 3.0 36.8 + - + +
43A GLU* 2.9 36.1 - - + +
45A ARG* 1.3 74.4 - - - +
47A ARG* 1.3 64.9 + - + +
49A ALA* 4.0 4.1 - - - +
50A GLU* 3.0 34.6 + - - +
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Residues in contact with ARG 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 GLU* 3.0 22.2 + - + +
44A GLU* 3.3 31.4 - - - +
46A MET* 1.3 79.7 - - + +
48A MET* 1.3 68.4 + - + +
50A GLU* 3.3 12.3 - - - +
51A GLY 2.9 31.6 + - - +
52A GLY* 4.9 5.6 - - - -
54A THR* 5.0 4.9 - - - +
56A GLU* 3.2 28.9 + - - +
57A ASP* 3.1 44.1 + - - +
60A THR* 3.4 18.8 + - - +
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Residues in contact with MET 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 GLU* 2.8 31.9 + - - +
45A ARG* 3.8 11.0 - - - +
47A ARG* 1.3 80.5 - - + +
49A ALA* 1.3 62.1 + - - +
51A GLY* 2.9 20.0 + - - -
57A ASP* 5.0 10.3 - - - +
60A THR* 4.9 8.7 - - + -
61A PHE* 4.0 36.6 - - + -
65A PRO* 3.4 35.2 - - + -
66A SER* 6.5 0.7 - - - -
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Residues in contact with ALA 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 ARG 3.0 18.4 + - - +
46A MET* 4.1 4.7 - - - +
48A MET* 1.3 77.1 - - - +
50A GLU* 1.3 62.2 + - - +
51A GLY* 3.2 1.4 + - - -
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Residues in contact with GLU 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 MET 3.0 24.8 + - - +
47A ARG* 3.3 17.4 - - - +
49A ALA* 1.3 76.4 - - - +
51A GLY* 1.3 69.3 + - - +
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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