Contacts of the helix formed by residues 34 - 53 (chain A) in PDB entry 2LOS
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.5 9.8 - - - +
27A ILE* 6.6 0.2 - - - -
30A VAL* 4.4 14.4 - - - +
32A ALA* 3.1 8.3 + - - -
33A GLY* 1.3 73.6 - - - +
35A VAL* 1.3 59.2 + - - +
36A PRO* 3.5 3.9 - - - +
37A SER* 3.0 33.3 + - - -
38A LEU* 2.7 39.8 + - - +
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Residues in contact with VAL 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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33A GLY 2.7 13.2 + - - +
34A SER* 1.3 72.0 - - - +
36A PRO* 1.4 74.0 - - + +
38A LEU* 4.3 1.0 - - - +
39A ALA* 2.9 30.2 + - + +
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Residues in contact with PRO 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 SER* 3.6 4.0 - - - +
35A VAL* 1.4 102.4 - - + +
37A SER* 1.3 58.0 + - - +
39A ALA* 3.3 6.1 + - + +
40A ALA* 2.7 35.8 + - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.6 11.5 - - - +
34A SER* 3.0 27.3 + - - -
36A PRO* 1.3 81.6 - - - +
38A LEU* 1.3 56.8 + - - +
40A ALA* 2.7 28.8 + - - +
41A GLY* 2.8 10.0 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 5.8 4.5 - - - +
34A SER* 2.7 27.4 + - - +
35A VAL 4.3 0.9 - - - +
37A SER* 1.3 78.4 - - - +
39A ALA* 1.3 57.9 + - - +
41A GLY* 2.7 23.0 + - - +
42A LEU* 2.9 30.0 + - + -
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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
----------------------------------------------------------
35A VAL* 2.9 24.4 + - + +
36A PRO* 3.5 7.2 - - + +
38A LEU* 1.3 80.6 - - - +
40A ALA* 1.3 58.0 + - - +
42A LEU* 3.3 9.3 + - - +
43A LEU* 3.1 32.6 + - + +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO 2.7 14.4 + - - +
37A SER* 2.7 15.7 + - - +
39A ALA* 1.3 76.4 - - - +
41A GLY* 1.3 56.9 + - - +
43A LEU* 4.1 3.9 - - - +
44A PHE* 3.0 34.8 + - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER 2.8 7.9 + - - -
38A LEU* 2.7 10.8 + - - -
40A ALA* 1.3 76.2 - - - +
42A LEU* 1.3 54.2 + - - -
44A PHE* 4.7 2.5 - - - -
45A GLY* 2.6 33.1 + - - -
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Residues in contact with LEU 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 LEU* 2.9 25.9 + - + +
39A ALA* 3.7 11.4 - - - +
40A ALA 3.2 0.2 - - - -
41A GLY* 1.3 73.8 - - - +
43A LEU* 1.3 72.4 - - + +
45A GLY* 2.9 8.8 + - - -
46A SER* 3.0 20.7 + - - +
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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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39A ALA* 3.1 15.8 + - + +
40A ALA* 4.1 4.0 - - - +
42A LEU* 1.3 87.4 - - + +
44A PHE* 1.3 62.3 + - - +
46A SER* 3.3 6.1 + - - +
47A LEU* 3.0 46.3 + - + +
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Residues in contact with PHE 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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15A PHE* 6.2 4.0 - + - -
40A ALA 3.0 20.3 + - - +
41A GLY* 4.4 2.2 - - - +
43A LEU* 1.3 77.2 - - - +
45A GLY* 1.3 51.0 + - - +
47A LEU* 4.2 12.3 - - + -
48A ALA* 2.6 48.4 + - + +
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Residues in contact with GLY 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 GLY 2.6 27.2 + - - -
42A LEU* 2.9 4.8 + - - -
44A PHE* 1.3 72.8 - - - +
46A SER* 1.3 64.3 + - - -
48A ALA* 3.1 6.5 + - - +
49A GLY* 3.0 19.1 + - - -
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Residues in contact with SER 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 LEU* 3.0 14.0 + - - +
43A LEU* 3.3 10.7 + - - +
45A GLY* 1.3 70.3 - - - +
47A LEU* 1.3 70.2 + - - +
49A GLY* 4.5 0.7 - - - +
50A LEU* 2.6 59.0 + - - +
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Residues in contact with LEU 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* 3.0 35.1 + - + +
44A PHE* 4.2 14.1 - - + +
46A SER* 1.3 87.8 + - - +
48A ALA* 1.3 55.9 + - - +
50A LEU* 4.8 1.6 - - - -
51A GLY* 2.7 33.0 + - - +
52A ALA 3.7 0.3 + - - -
56A SER* 4.9 14.9 - - - +
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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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12A TRP* 5.9 2.0 - - + -
44A PHE* 2.6 36.5 + - + +
45A GLY* 3.2 7.9 - - - +
46A SER 3.0 0.4 - - - -
47A LEU* 1.3 71.6 - - - +
49A GLY* 1.3 53.6 + - - +
52A ALA* 2.6 42.3 + - - +
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Residues in contact with GLY 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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12A TRP* 5.7 2.2 - - - -
45A GLY 3.0 12.5 + - - -
46A SER* 3.8 1.1 - - - -
48A ALA* 1.3 73.2 - - - +
50A LEU* 1.3 68.4 + - - +
53A TYR* 2.9 60.9 + - - -
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Residues in contact with LEU 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 SER* 2.6 39.0 + - - +
47A LEU* 4.8 1.3 - - - -
49A GLY* 1.3 72.5 - - - -
51A GLY* 1.3 53.9 + - - +
53A TYR* 2.6 13.9 + - + -
54A GLN* 2.5 64.7 + - + +
55A LEU 6.0 0.7 - - - +
79A ARG* 5.4 10.5 - - - +
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Residues in contact with GLY 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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47A LEU* 2.7 25.7 + - - +
50A LEU* 1.3 76.3 - - - +
52A ALA* 1.3 61.1 + - - +
53A TYR 3.2 0.2 + - - -
55A LEU 4.5 1.0 + - - -
56A SER* 3.3 29.4 - - - -
57A GLN* 3.6 23.0 + - - +
62A VAL* 3.7 8.8 - - - +
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Residues in contact with ALA 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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12A TRP* 4.3 14.4 - - + -
48A ALA 2.6 25.7 + - - +
50A LEU 3.1 0.2 - - - -
51A GLY* 1.3 74.0 - - - +
53A TYR* 1.3 80.6 + - + +
57A GLN* 5.3 4.6 - - - +
61A ASN* 5.8 1.2 - - - +
62A VAL* 4.6 4.0 + - - +
65A PHE* 3.3 19.3 - - + -
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Residues in contact with TYR 53 (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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12A TRP* 3.9 22.3 - + - -
49A GLY* 2.9 39.1 - - - -
50A LEU* 2.6 14.6 + - + -
52A ALA* 1.3 89.3 - - + +
54A GLN* 1.3 67.6 + - - +
62A VAL* 4.7 1.3 - - - -
65A PHE* 3.1 57.2 - + + +
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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