Contacts of the helix formed by residues 41 - 61 (chain A) in PDB entry 2LKX
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 41 (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* 3.6 9.4 - - - +
40A LEU* 1.3 79.0 - - - +
42A GLU* 1.3 66.1 + - - +
43A ALA* 3.3 3.4 - - - +
44A ARG* 3.0 50.3 + - - +
45A VAL* 3.4 4.7 + - - +
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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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28A MET* 4.4 11.1 - - + +
31A ARG* 2.7 62.8 + - + +
32A GLU* 4.2 18.8 - - + +
35A ALA* 3.9 2.6 - - - +
41A THR* 1.3 72.4 - - - +
43A ALA* 1.3 60.0 + - - +
45A VAL* 3.2 6.3 + - - +
46A ARG* 2.8 58.5 + - - -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.3 2.6 - - - +
42A GLU* 1.3 86.1 + - - +
44A ARG* 1.3 64.9 + - + +
46A ARG* 3.2 14.6 + - - +
47A VAL* 2.9 38.3 + - + +
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.4 8.7 - - + -
40A LEU* 4.1 25.7 - - + +
41A THR* 3.0 35.4 + - - +
43A ALA* 1.3 80.9 - - - +
45A VAL* 1.3 61.7 + - - +
47A VAL* 3.5 13.8 - - - +
48A TRP* 3.2 23.6 + - - +
73B A 5.4 4.9 - - - -
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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
----------------------------------------------------------
16A LEU* 4.2 6.7 - - + -
31A ARG* 3.6 30.7 - - + +
34A ILE* 3.8 38.4 - - + +
35A ALA* 3.9 12.1 - - + +
38A THR* 5.1 0.4 - - - +
40A LEU* 4.7 10.1 - - + -
41A THR 3.4 9.8 + - - +
42A GLU 3.2 6.4 + - - +
44A ARG* 1.3 74.9 - - - +
46A ARG* 1.3 56.7 + - - +
48A TRP* 3.3 6.6 + - - +
49A PHE* 2.9 49.2 + - + -
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Residues in contact with ARG 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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31A ARG* 3.6 27.7 - - - +
42A GLU* 2.8 51.7 + - - +
43A ALA* 3.2 17.0 + - - +
45A VAL* 1.3 76.0 - - - +
47A VAL* 1.3 58.8 + - + +
49A PHE* 3.2 4.3 + - - +
50A LYS* 2.9 37.2 + - + +
81C G 4.4 31.4 + - - +
82C G 4.3 14.3 + - - +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 5.5 1.3 - - + -
43A ALA* 2.9 25.7 + - + +
44A ARG* 3.5 18.2 - - - +
46A ARG* 1.3 70.9 - - + +
48A TRP* 1.3 66.4 + - - +
50A LYS* 4.2 7.6 - - + -
51A ASN* 2.8 35.3 + - - +
72B A 5.4 1.8 - - + -
73B A 3.7 35.9 - - + +
74B T 3.6 29.8 - - + +
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Residues in contact with TRP 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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8A PHE* 3.8 36.0 - + + -
13A LEU* 3.6 28.3 - - + +
16A LEU* 3.6 53.8 - - + +
17A GLU* 4.0 11.0 - - + -
20A PHE* 4.4 7.9 - + + -
44A ARG 3.2 19.2 + - - +
45A VAL* 3.3 6.7 + - - +
47A VAL* 1.3 77.6 - - - +
49A PHE* 1.3 78.0 + + - +
51A ASN* 3.6 1.3 - - - +
52A ARG* 2.8 91.2 + - + +
72B A 5.0 5.2 + - - -
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Residues in contact with PHE 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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16A LEU* 4.0 29.2 - - + -
19A THR* 4.4 9.2 - - + -
20A PHE* 3.8 22.7 - + + -
23A ASN 3.4 25.6 - - - -
24A ARG 3.7 11.4 - - - -
26A PRO* 3.5 30.7 - - + -
31A ARG* 5.5 2.2 - - - -
34A ILE* 4.2 5.4 - - + -
45A VAL* 2.9 46.4 + - + +
46A ARG* 3.7 6.5 - - - +
48A TRP* 1.3 84.5 - + - +
50A LYS* 1.3 62.4 + - - +
52A ARG* 3.2 4.6 + - - +
53A ARG* 3.1 36.6 + - - +
82C G 5.1 2.7 - - - +
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Residues in contact with LYS 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 ARG* 2.9 28.1 + - + +
47A VAL* 3.9 9.6 - - + +
49A PHE* 1.3 71.8 - - - +
51A ASN* 1.3 61.7 + - - +
53A ARG* 3.5 22.9 + - - +
54A ALA* 2.9 31.1 + - - +
74B T 3.4 32.2 + - + +
75B C 3.3 9.5 - - - +
82C G 4.7 10.7 + - + +
83C G 3.1 38.0 + - + +
84C G 2.9 24.0 + - - -
85C A 5.1 0.9 - - - +
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Residues in contact with ASN 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 VAL* 2.8 31.9 + - - +
48A TRP* 3.8 2.5 - - - +
50A LYS* 1.3 79.0 - - - +
52A ARG* 1.3 55.7 + - - +
54A ALA* 4.2 4.0 - - - +
55A LYS* 2.8 68.5 + - + +
72B A 3.3 33.8 - - - +
73B A 2.9 37.6 + - - +
74B T 4.5 4.0 - - - +
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Residues in contact with ARG 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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20A PHE* 3.7 31.7 - - + -
48A TRP* 2.8 94.4 + - + +
49A PHE 3.2 7.1 + - - +
51A ASN* 1.3 74.1 + - - +
53A ARG* 1.3 58.2 + - - +
55A LYS* 3.8 8.7 - - - +
56A TRP* 2.9 29.6 + - - +
71B T 4.9 1.6 - - - -
72B A 2.8 36.6 + - - -
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Residues in contact with ARG 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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20A PHE* 4.0 18.6 - - + -
24A ARG* 2.9 39.5 + - - +
25A TYR* 3.4 41.0 - - - +
26A PRO* 4.9 0.8 - - - +
49A PHE* 3.1 26.8 + - - +
50A LYS* 3.7 23.7 - - - +
52A ARG* 1.3 72.1 - - - +
54A ALA* 1.3 63.0 + - - +
56A TRP* 3.4 15.3 - - + +
57A ARG* 3.0 28.6 + - + +
82C G 2.8 48.5 + - - +
83C G 2.9 23.6 + - - +
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Residues in contact with ALA 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 LYS* 2.9 23.4 + - - +
51A ASN* 3.8 8.3 - - - +
53A ARG* 1.3 72.2 - - - +
55A LYS* 1.3 62.2 + - + +
57A ARG* 3.3 6.9 + - - +
58A LYS* 2.8 46.5 + - + +
73B A 6.3 0.2 - - - +
83C G 6.2 1.6 - - + -
84C G 4.9 19.7 - - + +
85C A 5.5 6.3 - - - +
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Residues in contact with LYS 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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51A ASN* 2.8 50.5 + - + +
52A ARG* 3.8 9.4 - - - +
54A ALA* 1.3 79.1 - - + +
56A TRP* 1.3 64.2 + - - +
57A ARG 3.4 0.2 - - - -
58A LYS* 4.0 19.6 - - + +
59A ARG* 3.2 35.9 + - + +
71B T 3.7 47.8 - - + +
72B A 2.9 27.8 + - - +
73B A 3.6 9.7 - - - +
85C A 5.7 0.4 - - - +
86C T 4.4 4.6 + - - -
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Residues in contact with TRP 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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20A PHE* 5.4 3.4 - - + -
24A ARG* 3.2 31.9 - - - +
25A TYR* 5.2 9.0 - - - -
52A ARG 2.9 19.0 + - - +
53A ARG* 3.4 16.2 - - + +
55A LYS* 1.3 75.4 - - - +
57A ARG* 1.3 98.3 + - + +
59A ARG* 3.7 0.3 - - - +
60A GLU* 2.8 52.2 + - + +
61A GLU 3.8 14.1 - - - -
62A PHE* 3.9 18.3 - - - +
63A ILE 3.1 20.4 + - - +
64A VAL* 3.6 15.9 - - + +
83C G 5.9 1.3 - - - -
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Residues in contact with ARG 57 (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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53A ARG 3.0 15.5 + - - +
54A ALA* 3.3 8.3 + - - +
56A TRP* 1.3 104.6 - - + +
58A LYS* 1.3 60.7 + - + +
59A ARG 3.1 3.5 + - - -
60A GLU 3.4 0.3 + - - -
61A GLU* 2.8 94.2 + - - +
62A PHE* 5.7 0.8 - - - +
83C G 4.9 3.6 - - - -
84C G 3.3 33.6 + - - +
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Residues in contact with LYS 58 (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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54A ALA* 2.8 33.2 + - + +
55A LYS* 4.3 20.0 - - + +
56A TRP 3.4 0.6 - - - -
57A ARG* 1.3 72.1 - - + +
59A ARG* 1.3 63.4 + - - +
61A GLU* 5.1 2.5 - - - +
71B T 4.7 20.0 - - + -
84C G 6.1 4.5 - - + +
85C A 5.1 13.9 + - - +
86C T 4.6 24.9 - - - +
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Residues in contact with ARG 59 (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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55A LYS* 3.2 27.3 + - + +
56A TRP 3.2 2.1 + - - +
57A ARG 3.2 1.1 - - - -
58A LYS* 1.3 84.2 - - + +
60A GLU* 1.3 68.0 + - + +
70B C 3.8 27.3 + - - +
71B T 2.8 38.6 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 2.8 36.5 + - + +
59A ARG* 1.3 83.9 - - + +
61A GLU* 1.3 54.6 + - - +
62A PHE* 2.7 20.9 + - - -
63A ILE* 3.2 56.4 + - + +
64A VAL* 5.3 1.2 - - - -
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Residues in contact with GLU 61 (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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56A TRP* 3.6 12.1 + - - -
57A ARG* 2.8 99.6 + - - +
58A LYS* 5.1 2.1 - - - +
60A GLU* 1.3 67.3 - - - +
62A PHE* 1.3 64.1 + - + +
84C G 4.3 3.6 + - - -
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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
------------------------------------------------------------
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