Contacts of the helix formed by residues 37 - 55 (chain A) in PDB entry 2L8K
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 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 ALA* 4.8 2.1 - - - +
36A LEU* 1.3 90.0 + - - +
38A SER* 1.3 70.4 + - - +
39A PHE* 3.2 3.1 - - + +
40A GLN* 2.9 30.6 + - - +
41A VAL* 2.9 29.1 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 1.3 78.0 - - - +
39A PHE* 1.3 62.2 + - - +
41A VAL* 4.3 4.2 - - - +
42A ALA* 3.3 21.7 + - - +
45A ARG* 5.4 0.2 + - - -
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Residues in contact with PHE 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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37A THR* 3.2 3.4 - - + +
38A SER* 1.3 77.7 - - - +
40A GLN* 1.3 65.5 + - - +
42A ALA* 3.4 7.0 + - + -
43A GLN* 2.8 56.3 + - + +
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.3 40.2 - - + -
37A THR* 2.9 31.6 + - - +
39A PHE* 1.3 83.9 - - - +
41A VAL* 1.3 63.8 + - - +
43A GLN* 2.9 43.8 + - - +
44A TYR* 3.2 8.5 + - - +
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Residues in contact with VAL 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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27A ARG* 4.4 24.5 - - - +
35A ALA* 4.9 1.8 - - + -
36A LEU* 4.8 8.7 - - + +
37A THR 2.9 26.8 + - - +
38A SER* 4.3 4.9 - - - +
40A GLN* 1.3 73.0 - - - +
42A ALA* 1.3 62.6 + - - +
44A TYR* 3.4 6.5 + - - +
45A ARG* 3.1 37.0 + - - +
71A PHE* 4.3 8.9 - - + -
72A ALA* 4.0 24.5 - - + -
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Residues in contact with ALA 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 SER 3.3 18.1 + - - +
39A PHE* 3.7 9.6 - - + +
40A GLN 3.2 0.6 - - - -
41A VAL* 1.3 76.5 - - - +
43A GLN* 1.3 61.0 + - - +
45A ARG* 3.1 30.3 + - - +
46A ASN* 2.9 35.5 + - - +
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Residues in contact with GLN 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 PHE* 2.8 34.1 + - + +
40A GLN* 3.1 33.4 + - - +
42A ALA* 1.3 75.6 - - - +
44A TYR* 1.3 63.4 + - - +
46A ASN* 3.0 21.1 + - + +
47A ILE* 3.2 18.2 + - + +
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Residues in contact with TYR 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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20A VAL* 5.8 0.7 - - + -
40A GLN 3.2 7.3 + - - +
41A VAL* 3.9 7.9 - - - +
43A GLN* 1.3 79.2 - - - +
45A ARG* 1.3 62.2 + - - +
47A ILE* 3.2 36.1 + - + +
48A LEU* 3.5 36.4 + - + +
71A PHE* 3.4 34.1 - + + -
84A VAL* 6.1 0.7 - - + -
86A ILE* 3.9 45.2 - - + -
109A VAL* 5.8 1.2 - - - +
112A SER* 4.0 21.9 + - - -
113A ARG 4.3 0.2 + - - -
114A CYS* 3.2 36.2 - - - +
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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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38A SER 5.4 0.2 + - - -
41A VAL* 3.1 24.2 + - - +
42A ALA* 3.2 32.2 - - - +
44A TYR* 1.3 81.5 - - - +
46A ASN* 1.3 56.5 + - - +
48A LEU* 5.4 0.7 - - - -
49A ASN* 2.8 32.9 + - - +
68A LEU* 3.4 44.1 - - + +
69A ALA* 5.0 7.0 + - - +
71A PHE* 3.3 42.7 + - + +
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Residues in contact with ASN 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 ALA* 2.9 16.5 + - - +
43A GLN* 3.0 12.5 + - - +
45A ARG* 1.3 74.4 - - - +
47A ILE* 1.3 59.5 + - - +
49A ASN* 4.0 13.9 + - - +
50A ALA* 2.8 34.3 + - - +
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Residues in contact with ILE 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 GLN* 3.2 14.7 + - + +
44A TYR* 3.2 36.1 - - + +
46A ASN* 1.3 79.2 - - + +
48A LEU* 1.3 76.6 + - + +
50A ALA* 3.4 9.3 + - - +
51A SER* 3.4 10.9 + - - -
109A VAL* 3.9 21.1 - - + +
110A GLY* 4.4 15.3 - - - +
112A SER* 4.1 15.0 - - - +
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Residues in contact with LEU 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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17A LEU* 3.6 38.6 - - + -
20A VAL* 4.8 10.8 - - + -
21A LEU* 5.2 1.1 - - + -
44A TYR* 3.5 42.9 + - + +
45A ARG* 5.4 0.2 - - - -
47A ILE* 1.3 88.5 - - + +
49A ASN* 1.3 62.1 + - - +
51A SER* 2.8 24.3 + - - -
52A LEU* 2.9 18.1 - - - +
68A LEU* 3.7 11.0 - - + -
71A PHE* 4.7 11.0 - - + -
109A VAL* 4.2 23.6 - - + +
114A CYS* 5.6 1.3 - - - -
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Residues in contact with ASN 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 2.8 23.2 + - - +
46A ASN* 3.9 13.7 + - - +
48A LEU* 1.3 77.8 - - - +
50A ALA* 1.3 56.1 + - - +
52A LEU* 3.2 19.3 + - - +
53A GLN* 2.6 38.8 + - - +
65A MET* 3.3 19.4 - - - +
68A LEU* 3.2 30.1 - - + +
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Residues in contact with ALA 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 ASN 2.8 21.2 + - - +
47A ILE* 3.6 6.1 - - - +
48A LEU 3.1 0.2 - - - -
49A ASN* 1.3 76.1 - - - +
51A SER* 1.3 53.7 + - - +
53A GLN* 2.9 29.6 - - + +
54A VAL* 2.7 29.5 - - + +
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Residues in contact with SER 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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7A ALA* 3.8 8.7 + - - +
9A LEU* 2.8 34.8 - - - +
14A PHE* 3.2 13.2 - - - -
17A LEU* 4.9 3.4 - - - -
47A ILE 3.4 6.4 + - - -
48A LEU* 2.8 19.3 + - - -
50A ALA* 1.3 80.9 - - - +
52A LEU* 1.3 63.9 + - - +
54A VAL* 3.0 18.6 - - - +
55A ASP* 3.1 7.4 + - - -
109A VAL* 4.7 6.9 - - - +
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Residues in contact with LEU 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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14A PHE* 3.9 13.0 - - + -
17A LEU* 4.4 13.0 - - + -
21A LEU* 5.6 0.4 - - + -
48A LEU 2.9 16.8 - - - +
49A ASN* 3.2 24.9 - - - +
50A ALA 3.2 0.2 - - - -
51A SER* 1.3 76.7 - - - +
53A GLN* 1.3 62.0 + - - +
55A ASP* 2.7 26.0 - - - +
61A SER* 3.4 13.9 - - - -
64A LEU* 3.4 29.2 - - + +
65A MET* 3.5 51.8 - - + +
68A LEU* 4.4 8.7 - - + -
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Residues in contact with GLN 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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49A ASN* 2.6 42.6 + - - +
50A ALA* 2.9 29.3 - - + +
52A LEU* 1.3 77.2 - - - +
54A VAL* 1.3 69.4 + - + +
55A ASP 2.9 8.7 + - - +
58A ALA* 6.1 1.2 - - - -
61A SER* 5.1 2.4 + - - -
65A MET* 3.2 16.0 - - + +
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Residues in contact with VAL 54 (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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7A ALA* 3.9 30.3 - - + +
8A ALA* 5.2 7.5 - - - +
50A ALA* 2.7 27.6 - - + +
51A SER* 3.0 23.6 - - - +
53A GLN* 1.3 76.4 - - + +
55A ASP* 1.3 68.7 + - - +
56A ARG* 4.5 2.4 - - - +
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Residues in contact with ASP 55 (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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8A ALA* 5.4 5.3 - - - +
9A LEU 3.3 10.3 - - - +
14A PHE* 2.8 48.8 - - + -
51A SER 3.1 6.9 + - - -
52A LEU 2.7 19.0 + - - +
53A GLN 2.9 8.4 + - - +
54A VAL* 1.3 87.7 - - - +
56A ARG* 1.3 75.4 + - - +
57A ASP* 3.7 27.8 + - - +
58A ALA* 5.1 1.4 + - - -
60A ARG* 4.9 3.1 - - - +
61A SER 4.8 4.5 + - - -
64A LEU* 5.3 0.2 - - - +
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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