Contacts of the helix formed by residues 44 - 60 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR 5.6 0.7 - - - +
43A HIS* 1.3 75.6 - - - +
45A LYS* 1.3 65.2 + - - +
46A GLU* 3.4 17.4 + - - +
47A GLN* 2.8 41.0 + - - +
48A ILE* 3.0 22.5 + - - +
45B LYS* 4.0 6.3 - - - +
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Residues in contact with LYS 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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44A THR* 1.3 73.4 - - - +
46A GLU* 1.3 72.7 + - - +
48A ILE* 3.4 4.6 + - + +
49A LEU* 3.0 35.6 + - - +
40B PRO* 3.0 29.3 + - + +
41B GLU 5.5 0.6 - - - -
43B HIS 3.0 22.8 + - - -
44B THR* 4.2 2.7 - - - +
45B LYS* 3.6 38.6 - - + +
48B ILE* 3.6 31.9 - - + -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.2 16.3 + - - +
45A LYS* 1.3 96.9 + - - +
47A GLN* 1.3 61.5 + - + +
49A LEU* 3.4 11.6 + - + +
50A GLU* 3.1 27.0 + - - +
97A EMC 4.3 2.1 - - - +
40B PRO* 5.4 4.0 - - - +
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Residues in contact with GLN 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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42A THR 3.9 3.3 + - - +
43A HIS* 3.2 30.9 - - + -
44A THR* 2.8 51.6 + - - +
46A GLU* 1.3 78.5 - - + +
48A ILE* 1.3 61.5 + - - +
50A GLU* 3.3 10.3 + - - +
51A LEU* 3.2 25.8 + - - +
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Residues in contact with ILE 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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38A LEU* 3.8 30.7 - - + +
40A PRO* 3.8 33.2 - - + -
43A HIS* 3.9 7.0 - - + +
44A THR 3.0 17.4 + - - +
45A LYS* 3.6 9.6 - - + +
47A GLN* 1.3 72.2 - - - +
49A LEU* 1.3 65.4 + - - +
51A LEU* 3.0 12.5 + - - +
52A VAL* 3.0 24.0 + - + +
45B LYS* 4.0 18.2 - - + -
48B ILE* 4.5 17.5 - - + -
49B LEU* 4.0 27.1 - - + -
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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
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45A LYS 3.0 21.6 + - - +
46A GLU* 3.8 6.7 - - + +
47A GLN 3.4 0.2 - - - -
48A ILE* 1.3 75.3 - - - +
50A GLU* 1.3 57.1 + - - +
52A VAL* 3.3 5.7 + - + +
53A VAL* 2.9 33.4 + - - +
97A EMC 3.5 24.2 - - + -
34B CYS* 4.0 6.9 - - - -
35B ARG* 5.5 1.3 - - + +
38B LEU* 3.4 42.2 - - + -
40B PRO* 3.6 36.6 - - + -
48B ILE* 4.1 19.1 - - + -
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Residues in contact with GLU 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 GLU 3.1 17.2 + - - +
47A GLN* 3.5 12.6 - - - +
48A ILE 3.3 0.2 - - - -
49A LEU* 1.3 76.7 - - - +
51A LEU* 1.3 58.0 + - + +
53A VAL* 3.5 5.7 + - - +
54A LEU* 2.9 30.7 + - - +
75A GLU 5.5 0.4 - - - +
76A ASN* 3.9 17.7 - - + +
77A GLY* 3.5 20.6 + - - -
78A GLU* 4.5 2.1 + - - +
97A EMC 3.1 18.4 - - + +
31B ARG* 2.5 44.8 + - - +
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Residues in contact with LEU 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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5A PRO* 5.8 6.7 - - + -
37A TRP* 3.8 25.5 - - + +
38A LEU* 3.8 30.5 - - + +
39A ARG* 6.0 0.4 - - - +
43A HIS* 4.1 28.0 - - + +
47A GLN 3.2 13.7 + - - +
48A ILE* 3.0 10.0 + - - +
50A GLU* 1.3 75.8 - - + +
52A VAL* 1.3 59.1 + - - +
54A LEU* 3.4 10.8 + - + +
55A GLU* 3.1 28.6 + - - +
75A GLU* 3.5 27.8 - - + +
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Residues in contact with VAL 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 ARG* 6.1 1.1 - - - +
37A TRP* 4.6 10.8 - - + -
38A LEU* 4.6 15.5 - - + -
48A ILE* 3.0 20.5 + - + +
49A LEU* 3.3 11.0 + - - +
51A LEU* 1.3 76.6 - - - +
53A VAL* 1.3 61.5 + - - +
55A GLU* 3.5 7.3 + - - +
56A GLN* 3.3 16.1 + - - +
12B PHE* 3.7 30.7 - - + -
13B ARG* 4.6 9.7 + - - +
34B CYS* 4.0 12.8 - - - -
37B TRP* 4.8 2.0 - - + -
38B LEU* 4.2 11.7 - - + -
48B ILE* 5.9 0.2 - - + -
52B VAL* 4.1 24.5 - - + -
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Residues in contact with VAL 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 2.9 20.9 + - - +
50A GLU* 3.8 9.2 - - - +
52A VAL* 1.3 71.5 - - - +
54A LEU* 1.3 61.3 + - - +
56A GLN* 3.1 3.6 + - - +
57A PHE* 2.8 28.9 + - + +
77A GLY* 5.5 1.8 - - - -
97A EMC 4.2 5.4 - - + -
12B PHE* 4.3 6.7 - - - -
27B VAL* 4.2 15.0 - - + +
30B LEU* 4.1 19.5 - - + +
31B ARG* 3.9 34.8 - - + +
34B CYS* 3.8 29.2 - - + -
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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 GLU 2.9 19.0 + - - +
51A LEU* 3.6 13.7 - - + +
53A VAL* 1.3 76.6 - - - +
55A GLU* 1.3 65.6 + - - +
57A PHE* 3.1 7.3 + - + +
58A VAL* 3.0 40.8 + - + +
74A PRO* 3.4 30.1 - - + +
75A GLU 3.7 5.8 - - - +
76A ASN 3.7 31.4 - - - +
77A GLY* 4.2 10.3 - - - +
80A ALA* 3.7 16.6 - - + -
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Residues in contact with GLU 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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9A ARG* 2.9 49.9 + - - +
13A ARG* 2.7 47.0 + - - +
37A TRP* 3.4 14.2 - - + -
51A LEU 3.1 16.7 + - - +
52A VAL* 3.8 6.3 - - - +
53A VAL 3.3 0.2 - - - -
54A LEU* 1.3 78.3 - - - +
56A GLN* 1.3 59.0 + - - +
58A VAL* 3.9 4.8 - - - +
59A ALA* 2.9 27.1 + - + +
13B ARG* 4.3 7.0 + - - +
94B PEG 3.9 15.3 - - - +
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Residues in contact with GLN 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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52A VAL 3.3 1.8 + - - -
53A VAL 3.1 5.1 + - - +
55A GLU* 1.3 75.7 - - - +
57A PHE* 1.3 67.2 + - - +
59A ALA* 3.1 7.7 + - - +
60A ILE* 3.1 43.1 + - + +
12B PHE* 3.6 40.3 + - + +
13B ARG* 2.9 64.4 + - - +
15B PHE 4.8 0.2 + - - -
30B LEU* 3.9 13.7 - - + -
94B PEG 4.1 13.5 - - - -
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Residues in contact with PHE 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 VAL 2.8 17.0 + - - +
54A LEU* 3.6 7.6 - - + +
56A GLN* 1.3 79.9 - - - +
58A VAL* 1.3 68.0 + - + +
60A ILE* 3.3 19.9 + - + +
61A LEU* 3.5 18.4 + - + +
77A GLY* 5.1 0.7 - - - -
80A ALA* 3.8 34.3 - - + -
81A VAL* 4.4 0.4 - - + -
84A LEU* 3.5 30.7 - - + -
17B TYR* 3.7 21.8 - + - -
23B PRO* 3.8 17.9 - - + -
26B ALA* 4.1 6.5 - - + -
27B VAL* 3.6 30.5 - - + -
30B LEU* 3.6 21.7 - - + +
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Residues in contact with VAL 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 LEU* 3.0 39.6 + - + +
55A GLU* 3.9 5.2 - - - +
57A PHE* 1.3 77.4 - - + +
59A ALA* 1.3 64.2 + - - +
60A ILE 3.2 0.7 + - - -
61A LEU* 3.2 14.5 + - - +
66A GLN* 3.1 34.5 + - + +
69A VAL* 4.0 22.0 - - + -
70A ARG* 3.3 42.8 - - + +
74A PRO* 5.1 2.2 - - + -
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Residues in contact with ALA 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 GLU 2.9 19.2 + - - +
56A GLN* 3.1 19.4 + - - +
58A VAL* 1.3 78.6 - - - +
60A ILE* 1.3 59.5 + - + +
61A LEU 4.2 0.5 - - - +
66A GLN* 3.3 19.5 + - - +
70A ARG* 5.6 1.3 - - - +
94B PEG 3.9 20.2 - - - +
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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
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56A GLN* 3.1 31.9 + - - +
57A PHE* 3.3 16.2 - - + +
59A ALA* 1.3 76.3 - - - +
61A LEU* 1.3 65.5 + - - +
62A PRO* 3.6 0.5 - - - +
13B ARG 5.1 1.1 - - - +
15B PHE* 3.5 35.9 - - + +
16B GLY* 5.1 1.1 - - - -
17B TYR* 3.4 46.6 + - + +
26B ALA* 5.1 0.7 - - + -
30B LEU* 3.8 28.0 - - + -
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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