Contacts of the helix formed by residues 44 - 61 (chain B) in PDB entry 3LHR
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 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 4.2 7.2 - - - +
42B THR 5.4 1.3 - - - +
43B HIS* 1.3 75.0 - - - +
45B LYS* 1.3 64.5 + - - +
46B GLU* 3.4 9.9 + - - +
47B GLN* 2.9 39.3 + - - +
48B ILE* 3.0 22.6 + - - +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 2.5 42.1 + - - -
41A GLU 5.1 0.4 - - - -
43A HIS 2.8 15.6 + - - +
44A THR* 4.4 2.5 - - - +
45A LYS* 3.6 52.2 - - + +
48A ILE* 4.0 11.4 - - + +
44B THR* 1.3 72.4 - - - +
46B GLU* 1.3 68.4 + - + +
48B ILE* 3.3 4.3 + - - +
49B LEU* 3.0 31.9 + - + +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.6 44.4 + - - -
40A PRO* 4.6 4.0 - - - +
96A EMC 4.5 6.6 - - - +
44B THR* 3.2 10.1 + - - +
45B LYS* 1.3 81.0 - - + +
47B GLN* 1.3 59.7 + - + +
49B LEU* 3.4 13.4 + - - +
50B GLU* 2.9 29.1 + - - +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR 4.0 3.5 - - - +
43B HIS* 3.3 30.6 - - + -
44B THR* 2.9 45.2 + - - +
46B GLU* 1.3 77.0 - - + +
48B ILE* 1.3 63.7 + - - +
50B GLU* 3.4 8.1 + - - +
51B LEU* 3.2 28.0 + - + +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 3.6 37.9 - - + +
48A ILE* 4.5 17.0 - - + -
49A LEU* 4.1 25.4 - - + -
52A VAL* 5.9 0.2 - - + -
38B LEU* 3.8 30.5 - - + +
40B PRO* 4.0 20.0 - - + -
43B HIS* 3.8 6.3 - - + +
44B THR 3.0 13.5 + - - +
45B LYS* 3.6 8.3 - - - +
47B GLN* 1.3 76.2 - - - +
49B LEU* 1.3 67.0 + - - +
51B LEU* 3.1 11.3 + - - +
52B VAL* 3.0 25.6 + - + +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A CYS* 4.2 5.6 - - - -
35A ARG* 4.2 8.7 - - + +
38A LEU* 3.7 33.4 - - + -
40A PRO* 3.6 31.0 - - + -
48A ILE* 4.0 25.4 - - + -
96A EMC 3.6 16.2 - - + -
45B LYS 3.0 23.7 + - - +
46B GLU* 3.8 24.0 - - - +
48B ILE* 1.3 75.9 - - + +
50B GLU* 1.3 63.9 + - - +
52B VAL* 3.1 8.4 + - - +
53B VAL* 3.0 25.5 + - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 5.2 0.2 - - - +
31A ARG* 2.7 42.6 + - - -
96A EMC 3.3 16.0 - - - +
46B GLU 2.9 17.5 + - - +
47B GLN* 3.6 8.5 - - - +
49B LEU* 1.3 77.8 - - - +
51B LEU* 1.3 56.2 + - + +
53B VAL* 3.5 4.0 + - - +
54B LEU* 2.8 28.8 + - - +
75B GLU 5.1 0.9 - - - +
76B ASN* 3.6 24.2 - - + +
77B GLY* 2.7 25.0 + - - -
78B GLU* 3.8 1.2 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 6.4 3.6 - - + -
37B TRP* 4.0 26.2 - - + +
38B LEU* 3.9 24.7 - - + +
43B HIS* 3.9 30.7 - - + +
47B GLN 3.2 15.4 + - - +
48B ILE* 3.1 8.8 + - - +
50B GLU* 1.3 75.9 - - - +
52B VAL* 1.3 57.9 + - - +
54B LEU* 3.6 10.4 - - + +
55B GLU* 3.0 29.8 + - - +
75B GLU* 3.3 31.0 - - + +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.8 28.2 - - + -
13A ARG* 4.5 10.8 + - - +
34A CYS* 4.1 3.1 - - - -
37A TRP* 4.8 2.9 - - + -
38A LEU* 4.1 21.8 - - + -
48A ILE* 6.0 0.2 - - + -
52A VAL* 4.1 23.3 - - + -
13B ARG* 6.0 1.6 - - - +
37B TRP* 4.7 11.2 - - + -
38B LEU* 4.5 16.4 - - + -
48B ILE* 3.0 20.4 + - + +
49B LEU* 3.5 9.2 - - - +
51B LEU* 1.3 76.9 - - - +
53B VAL* 1.3 61.9 + - - +
55B GLU* 3.4 7.2 + - - +
56B GLN* 3.3 16.8 + - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.2 6.3 - - + -
27A VAL* 4.0 23.6 - - + +
30A LEU* 3.9 22.5 - - + +
31A ARG* 3.9 14.1 - - + +
34A CYS* 3.6 23.1 - - + -
96A EMC 2.9 33.2 - - + -
49B LEU 3.0 7.7 + - - +
50B GLU* 3.7 10.5 - - - +
52B VAL* 1.3 72.4 - - - +
54B LEU* 1.3 67.8 + - - +
56B GLN* 3.2 3.8 + - - +
57B PHE* 2.8 22.2 + - + +
77B GLY* 5.5 0.2 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 2.8 21.2 + - - +
51B LEU* 3.4 12.3 + - + +
53B VAL* 1.3 73.8 - - - +
55B GLU* 1.3 64.2 - - - +
57B PHE* 3.2 7.6 + - + +
58B VAL* 2.9 33.2 + - + +
74B PRO* 3.3 37.2 - - + +
75B GLU 3.8 4.5 - - - +
76B ASN 3.7 24.9 - - - +
77B GLY* 4.2 9.6 - - - +
80B ALA* 3.6 30.7 - - + -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.5 5.2 + - - +
9B ARG* 2.8 48.7 + - - +
13B ARG* 2.7 44.3 + - - +
37B TRP* 3.2 15.5 - - + -
51B LEU 3.0 17.1 + - - +
52B VAL* 3.7 6.6 - - - +
53B VAL 3.2 0.2 - - - -
54B LEU* 1.3 79.0 - - - +
56B GLN* 1.3 58.1 + - - +
58B VAL* 3.5 5.8 + - - +
59B ALA* 3.0 26.0 + - - +
94B PEG 3.6 16.0 - - - +
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.7 31.8 + - + +
13A ARG* 2.9 64.3 + - - +
15A PHE 4.5 0.8 + - - -
30A LEU* 3.8 23.8 - - + -
52B VAL 3.3 2.2 + - - -
53B VAL 3.2 5.0 + - - +
55B GLU* 1.3 77.8 - - - +
57B PHE* 1.3 66.4 + - - +
59B ALA* 3.1 10.6 + - - +
60B ILE* 3.1 44.1 + - + +
94B PEG 4.1 8.5 - - - +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.9 21.5 - + - -
23A PRO* 3.8 25.1 - - + -
26A ALA* 4.0 7.2 - - + -
27A VAL* 3.3 34.8 - - + -
30A LEU* 3.6 20.0 - - + +
53B VAL* 2.8 18.8 + - + +
54B LEU* 3.2 13.2 + - + +
56B GLN* 1.3 72.1 - - - +
58B VAL* 1.3 65.9 + - + +
60B ILE* 3.0 19.8 + - + +
61B LEU* 3.2 41.8 + - + +
77B GLY* 6.1 0.2 - - - -
80B ALA* 3.8 32.8 - - + -
81B VAL* 4.4 0.7 - - + -
84B LEU* 4.0 6.7 - - + -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 6.3 0.9 - - - +
54B LEU* 2.9 39.1 + - + +
55B GLU* 3.8 5.4 - - - +
57B PHE* 1.3 76.7 - - + +
59B ALA* 1.3 64.1 + - - +
60B ILE 3.1 1.0 + - - -
61B LEU* 3.3 12.4 + - + +
66B GLN* 2.9 33.0 + - + +
69B VAL* 4.1 20.4 - - + -
70B ARG* 3.8 30.1 - - + -
74B PRO* 4.8 3.4 - - + -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU 3.0 15.6 + - - +
56B GLN* 3.1 22.0 + - - +
58B VAL* 1.3 77.8 - - - +
60B ILE* 1.3 59.7 + - + +
61B LEU 3.5 1.1 - - - +
66B GLN* 3.7 13.5 + - - +
94B PEG 3.9 19.3 - - - +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG 5.1 0.7 - - - +
15A PHE* 3.7 25.8 - - + +
16A GLY* 4.1 4.9 - - - -
17A TYR* 3.3 52.6 - - + +
26A ALA* 4.8 1.8 - - + -
30A LEU* 4.1 21.1 - - + -
56B GLN* 3.4 34.5 - - - +
57B PHE* 3.0 22.6 + - + +
59B ALA* 1.3 77.3 - - + +
61B LEU* 1.3 66.9 + - - +
62B PRO 3.5 0.3 - - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.6 28.5 - - + -
57B PHE* 3.2 38.6 + - + +
58B VAL* 3.3 17.8 + - - +
59B ALA 4.5 0.9 - - - +
60B ILE* 1.3 79.2 - - - +
62B PRO* 1.3 73.9 - - + +
63B LYS* 3.5 1.4 + - - -
65B LEU* 4.1 6.1 - - + +
66B GLN* 3.8 32.8 + - - +
69B VAL* 3.7 35.2 - - + -
84B LEU* 3.9 11.9 - - + -
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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