Contacts of the helix formed by residues 36 - 60 (chain A) in PDB entry 2LLY
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 GLY 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.1 13.4 + - - +
35A CYS* 1.3 77.9 - - - +
37A GLU* 1.3 62.3 + - - +
38A LYS 3.0 4.4 + - - -
39A ILE* 3.3 25.7 + - - +
40A THR* 2.8 16.2 + - - -
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Residues in contact with GLU 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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28A VAL* 4.0 28.1 - - + +
31A LEU 5.1 1.9 - - - +
32A PRO* 5.2 5.2 - - + -
33A SER* 4.1 17.6 + - - +
34A GLU* 3.3 42.4 + - - +
36A GLY* 1.3 78.1 - - - +
38A LYS* 1.3 63.1 + - - +
40A THR* 3.0 15.8 + - + +
41A LEU* 3.0 24.3 + - - +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 5.2 5.5 - - - +
28A VAL* 5.4 4.9 - - + +
29A PHE* 3.5 41.8 - - + -
34A GLU 4.7 0.4 + - - -
35A CYS 4.3 12.7 + - - +
36A GLY 3.0 0.4 - - - -
37A GLU* 1.3 80.9 - - - +
39A ILE* 1.3 70.1 + - + +
41A LEU* 3.2 9.1 + - - +
42A CYS* 3.2 24.9 + - - +
85A ILE* 3.6 34.1 - - - +
89A VAL* 4.8 10.6 - - + +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 4.8 4.3 - - - +
36A GLY* 3.3 24.0 + - - +
38A LYS* 1.3 81.5 - - + +
40A THR* 1.3 61.8 + - - +
42A CYS* 3.3 10.5 + - + +
43A ILE* 3.1 43.0 + - + +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 2.8 17.2 + - - -
37A GLU* 3.0 20.2 + - + -
39A ILE* 1.3 79.5 - - - +
41A LEU* 1.3 59.5 + - - +
43A ILE* 3.7 7.8 + - - +
44A SER* 2.8 29.8 + - - +
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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
----------------------------------------------------------
24A LEU* 3.9 30.3 - - + +
25A THR* 3.6 26.0 - - + +
28A VAL* 3.5 44.6 - - + +
37A GLU 3.0 8.7 + - - +
38A LYS* 3.7 10.8 - - - +
40A THR* 1.3 74.1 - - - +
42A CYS* 1.3 66.5 + - - +
44A SER* 3.1 10.8 + - - +
45A VAL* 3.0 37.5 + - + +
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Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.2 20.3 + - - +
39A ILE* 3.3 15.5 + - - +
41A LEU* 1.3 79.8 - - - +
43A ILE* 1.3 66.6 + - - +
45A VAL* 3.5 7.7 + - - +
46A LEU* 3.3 32.4 + - - +
85A ILE* 6.0 11.7 - - + -
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.1 35.1 + - + +
40A THR* 4.0 7.0 - - - +
42A CYS* 1.3 77.7 - - - +
44A SER* 1.3 66.4 + - - +
46A LEU* 3.2 16.2 + - + +
47A LEU* 3.2 35.7 + - + +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 6.0 5.4 - - - -
40A THR* 2.8 20.4 + - - +
41A LEU* 3.1 22.6 + - - +
43A ILE* 1.3 79.2 - - - +
45A VAL* 1.3 63.3 + - - +
47A LEU* 3.2 18.9 + - - +
48A SER* 3.4 11.4 + - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.5 28.0 - - + +
24A LEU* 5.7 4.0 - - + -
25A THR* 4.1 10.5 - - - +
41A LEU* 3.0 34.7 + - + +
42A CYS* 3.9 7.4 - - - +
44A SER* 1.3 75.4 - - - +
46A LEU* 1.3 56.4 + - - +
48A SER* 3.4 5.9 + - - +
49A LEU* 2.8 49.8 + - + +
81A VAL* 6.1 4.0 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.3 26.3 + - - +
43A ILE* 3.2 20.6 + - + +
44A SER 3.1 0.2 - - - -
45A VAL* 1.3 79.8 - - - +
47A LEU* 1.3 62.2 + - + +
49A LEU* 3.2 11.5 + - + +
50A THR* 2.7 42.1 + - - +
78A MET* 6.4 2.0 - - + -
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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 ILE* 3.2 31.6 + - + +
44A SER* 3.2 12.4 + - - +
46A LEU* 1.3 80.1 - - + +
48A SER* 1.3 58.1 + - - +
50A THR* 3.3 4.9 + - - -
51A VAL* 2.8 39.6 + - + +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 5.9 1.6 - - - +
20A LEU* 6.4 1.6 - - - -
21A ILE* 3.7 25.8 - - - +
44A SER 3.4 8.4 + - - -
45A VAL* 3.7 7.8 + - - -
46A LEU 3.3 0.4 - - - -
47A LEU* 1.3 75.5 - - - +
49A LEU* 1.3 65.0 + - - +
51A VAL* 2.9 8.9 + - - +
52A PHE* 2.8 35.7 + - - +
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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
----------------------------------------------------------
21A ILE* 5.7 9.0 - - + -
45A VAL* 2.8 43.7 + - + +
46A LEU* 3.5 11.7 - - + +
48A SER* 1.3 75.8 + - - +
50A THR* 1.3 56.5 + - - +
52A PHE* 4.3 10.0 - - + -
53A LEU* 3.0 27.9 + - - +
74A LEU* 4.6 11.3 - - + +
77A THR* 6.0 5.4 - - + -
78A MET* 3.7 47.1 - - + +
81A VAL* 5.2 11.2 - - + -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 2.7 34.4 + - - +
47A LEU* 3.8 5.1 - - - -
49A LEU* 1.3 75.4 - - - +
51A VAL* 1.3 64.6 + - - +
53A LEU* 3.8 17.3 - - + +
54A LEU* 3.4 25.9 + - + +
78A MET* 5.9 0.9 - - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 2.8 30.6 + - + +
48A SER* 2.9 9.8 + - - +
50A THR* 1.3 77.3 - - - +
52A PHE* 1.3 69.1 + - + +
53A LEU 3.4 0.3 + - - -
54A LEU* 3.6 3.7 + - - +
55A LEU* 3.4 21.0 + - + +
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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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13A ASN* 5.6 10.8 - - - -
14A LEU* 3.6 36.8 - - + -
17A PRO* 5.7 13.5 - - + -
48A SER* 2.8 16.7 + - - +
49A LEU* 4.6 8.7 - - + -
51A VAL* 1.3 76.4 - - + +
53A LEU* 1.3 69.2 + - - +
55A LEU* 3.4 15.1 - - + +
56A ILE* 3.3 40.2 + - + +
70A ILE* 3.6 15.5 - - + -
74A LEU* 4.0 28.5 - - + -
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Residues in contact with LEU 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 LEU 3.0 22.3 + - - +
50A THR* 3.8 19.1 - - + +
51A VAL 3.2 0.2 - - - -
52A PHE* 1.3 79.3 - - - +
54A LEU* 1.3 74.5 + - + +
56A ILE* 3.0 18.4 + - + +
57A THR* 3.1 27.7 + - + +
74A LEU* 4.6 22.7 - - + -
78A MET* 5.3 11.0 - - + -
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Residues in contact with LEU 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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50A THR* 3.4 18.3 + - + +
51A VAL* 4.0 4.3 - - - +
53A LEU* 1.3 85.9 - - + +
55A LEU* 1.3 58.8 + - - +
57A THR* 2.6 46.8 + - + +
58A GLU* 3.1 29.0 + - + +
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Residues in contact with LEU 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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13A ASN* 5.8 6.3 - - - +
51A VAL* 3.4 13.9 + - + +
52A PHE* 3.4 21.5 - - + +
53A LEU 3.2 0.4 - - - -
54A LEU* 1.3 78.8 - - - +
56A ILE* 1.3 60.6 + - + +
58A GLU* 3.0 31.7 + - + +
59A ILE* 3.4 18.7 + - + +
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Residues in contact with ILE 56 (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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10A TYR* 2.9 46.9 - - + +
13A ASN* 6.4 0.2 - - - +
14A LEU* 4.8 0.2 - - + -
52A PHE* 3.3 44.8 + - + +
53A LEU* 3.0 9.9 + - + +
55A LEU* 1.3 78.3 - - + +
57A THR* 1.3 60.0 + - + +
58A GLU 3.1 0.4 - - - -
59A ILE* 3.3 14.7 - - + +
61A PRO* 3.0 35.2 - - + +
70A ILE* 3.8 20.0 - - + -
74A LEU* 4.8 3.1 - - + -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.1 31.9 - - + +
54A LEU* 2.6 38.7 + - + +
56A ILE* 1.3 77.8 - - + +
58A GLU* 1.3 60.6 + - - +
60A ILE* 3.6 17.7 - - - +
61A PRO* 5.2 0.4 - - - -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.1 36.4 - - + +
55A LEU* 3.0 22.1 + - + +
57A THR* 1.3 77.8 + - - +
59A ILE* 1.3 62.9 + - + +
60A ILE* 2.9 21.2 - - - +
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.7 13.7 - - + +
6A LEU* 5.0 4.5 - - + -
10A TYR* 4.4 13.7 - - + -
55A LEU* 3.9 18.2 - - + +
56A ILE* 3.3 38.1 - - + +
58A GLU* 1.3 75.7 - - + +
60A ILE* 1.3 76.6 + - - +
61A PRO* 3.6 14.6 - - + -
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.8 7.3 - - - +
56A ILE 3.4 2.9 + - - -
57A THR* 3.6 15.9 - - - +
58A GLU* 2.9 25.3 - - - +
59A ILE* 1.3 82.2 - - - +
61A PRO* 1.3 70.4 - - - +
62A SER* 3.1 11.6 - - - +
63A THR* 4.0 28.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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