Contacts of the helix formed by residues 22 - 39 (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 GLY 22 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 4.5 8.5 + - - -
20A SER* 3.0 6.3 + - - -
21A PRO* 1.3 82.2 - - - +
23A PRO* 1.3 72.0 - - - +
25A GLU* 3.3 13.7 + - - +
26A ALA* 2.9 29.7 + - - +
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Residues in contact with PRO 23 (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 TYR* 3.6 19.3 - - - +
22A GLY* 1.3 81.6 - - - +
24A ARG* 1.3 66.5 + - - +
25A GLU* 4.7 0.4 - - - +
26A ALA* 3.2 5.0 + - + +
27A VAL* 3.0 29.3 + - - +
57B PHE* 3.8 12.1 - - + -
81B VAL* 4.0 11.2 - - + +
84B LEU* 3.6 40.8 - - + -
85B GLU* 5.3 6.3 - - + -
88B GLU* 5.8 7.0 - - - +
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Residues in contact with ARG 24 (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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22A GLY 3.4 0.2 - - - -
23A PRO* 1.3 79.4 - - - +
25A GLU* 1.3 70.0 + - + +
27A VAL* 3.5 2.4 + - - +
28A SER* 3.0 27.4 + - - -
31A ARG* 5.4 0.9 + - - -
95A CL 3.3 31.4 - - + +
78B GLU* 2.9 41.4 + - - -
81B VAL* 3.5 29.3 - - + +
82B THR* 3.8 4.4 - - - +
85B GLU* 2.8 46.6 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.5 4.6 + - - +
21A PRO* 3.9 35.3 - - + +
22A GLY* 3.3 23.8 - - - +
23A PRO* 4.7 0.3 - - - +
24A ARG* 1.3 84.1 + - + +
26A ALA* 1.3 61.6 + - - +
28A SER* 3.5 7.4 - - - -
29A GLN* 2.8 31.5 + - - +
94A MG 4.3 7.8 - - - -
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Residues in contact with ALA 26 (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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15A PHE* 3.8 12.4 - - + -
17A TYR* 4.4 13.7 - - + +
20A SER* 3.2 17.4 + - - -
22A GLY 2.9 18.3 + - - +
23A PRO* 3.6 7.0 - - + +
25A GLU* 1.3 78.9 - - - +
27A VAL* 1.3 57.2 + - - +
29A GLN* 3.4 2.4 + - - +
30A LEU* 2.9 33.4 + - - +
57B PHE* 4.0 17.0 - - + -
60B ILE* 4.8 2.7 - - + -
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Residues in contact with VAL 27 (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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23A PRO 3.0 10.9 + - - +
24A ARG 3.9 2.2 - - - +
26A ALA* 1.3 72.7 - - - +
28A SER* 1.3 60.6 + - - +
30A LEU* 3.3 8.7 + - - +
31A ARG* 2.9 61.6 + - - +
53B VAL* 4.0 11.2 - - + +
57B PHE* 3.3 39.3 - - + -
77B GLY* 4.2 12.1 - - - +
81B VAL* 3.5 26.7 - - + -
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Residues in contact with SER 28 (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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24A ARG* 3.0 20.8 + - - -
25A GLU* 3.5 9.2 - - - -
27A VAL* 1.3 77.3 - - - +
29A GLN* 1.3 62.1 + - - +
31A ARG* 3.4 18.6 + - - +
32A GLU* 3.3 34.1 + - - +
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Residues in contact with GLN 29 (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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11A ARG* 4.9 6.0 + - - -
15A PHE* 3.5 37.2 - - + -
20A SER* 4.4 1.8 - - - +
25A GLU 2.8 16.9 + - - +
26A ALA 3.8 3.8 - - - +
28A SER* 1.3 76.3 - - - +
30A LEU* 1.3 65.3 + - - +
32A GLU* 3.0 24.4 + - - +
33A LEU* 3.0 40.4 + - + +
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Residues in contact with LEU 30 (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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12A PHE* 3.7 41.3 - - + +
15A PHE* 3.8 23.1 - - + -
26A ALA 2.9 22.0 + - - +
27A VAL* 3.3 7.4 + - - +
29A GLN* 1.3 77.1 - - - +
31A ARG* 1.3 51.1 + - - +
33A LEU* 3.3 2.8 + - + +
34A CYS* 2.7 36.7 + - - +
53B VAL* 3.9 13.5 - - + +
56B GLN* 3.8 7.0 - - + +
57B PHE* 3.6 45.8 - - + +
60B ILE* 4.1 13.9 - - + -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 5.4 0.8 + - - +
27A VAL* 2.9 43.1 + - - +
28A SER* 3.5 20.8 - - - +
29A GLN 3.3 0.2 - - - -
30A LEU* 1.3 72.6 - - - +
32A GLU* 1.3 61.1 + - + +
34A CYS* 3.4 1.9 + - - +
35A ARG* 2.9 38.9 + - + +
96A EMC 3.6 23.2 - - + +
50B GLU* 2.7 40.3 + - - -
53B VAL* 3.9 14.8 - - + +
77B GLY 3.9 0.2 - - - -
78B GLU* 3.8 22.0 + - - +
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Residues in contact with GLU 32 (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 SER* 3.3 24.5 + - - +
29A GLN* 3.0 28.9 + - - +
31A ARG* 1.3 79.9 - - + +
33A LEU* 1.3 66.3 + - + +
35A ARG* 3.3 11.9 + - - +
36A LEU* 3.1 32.9 + - + +
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Residues in contact with LEU 33 (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 4.4 3.4 - - - +
11A ARG* 3.6 40.6 - - + +
12A PHE* 4.0 19.6 - - + +
15A PHE* 3.7 40.8 - - + -
29A GLN* 3.0 37.1 + - + +
30A LEU* 3.9 6.5 - - + +
32A GLU* 1.3 74.1 - - + +
34A CYS* 1.3 68.1 + - - +
36A LEU* 3.2 26.8 + - + +
37A TRP* 3.2 14.9 + - - +
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Residues in contact with CYS 34 (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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12A PHE* 3.9 17.6 - - + -
30A LEU 2.7 19.0 + - - +
31A ARG 3.5 5.6 - - - +
33A LEU* 1.3 77.7 - - - +
35A ARG* 1.3 60.7 + - - +
37A TRP* 3.2 5.3 + - - +
38A LEU* 2.9 51.8 + - - +
96A EMC 4.4 5.4 - - - -
49B LEU* 4.2 14.8 - - - -
52B VAL* 4.1 11.0 - - - -
53B VAL* 3.6 23.8 - - + -
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Residues in contact with ARG 35 (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* 2.9 27.1 + - - +
32A GLU* 3.6 11.4 - - - +
33A LEU 3.3 0.2 - - - -
34A CYS* 1.3 77.3 - - + +
36A LEU* 1.3 59.1 + - + +
38A LEU* 5.2 0.2 - - - -
39A ARG* 2.9 29.8 + - - +
40A PRO* 3.6 29.4 - - + +
41A GLU* 3.9 18.3 + - - +
96A EMC 4.0 20.8 - - + +
46B GLU* 2.6 42.6 + - - -
49B LEU* 4.4 4.8 - - + +
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Residues in contact with LEU 36 (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* 3.6 40.6 - - + -
32A GLU* 3.1 24.2 + - + +
33A LEU* 3.6 24.7 - - + +
34A CYS 3.2 0.6 - - - -
35A ARG* 1.3 77.4 - - + +
37A TRP* 1.3 60.3 + - - +
39A ARG* 3.5 17.1 - - - +
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Residues in contact with TRP 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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5A PRO* 3.6 25.1 + - + +
8A PHE* 3.8 7.8 - - + +
9A ARG* 3.6 50.0 - - + +
12A PHE* 3.9 24.5 - + + -
13A ARG* 4.0 11.9 - - - -
33A LEU 3.2 9.5 + - - +
34A CYS* 3.2 7.0 + - - +
36A LEU* 1.3 79.2 - - - +
38A LEU* 1.4 98.7 + - + +
39A ARG* 3.3 12.9 + - - -
51A LEU* 3.8 40.1 - - + +
52A VAL* 4.6 5.6 - - + -
55A GLU* 3.4 29.8 - - + -
52B VAL* 4.8 2.5 - - + -
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Residues in contact with LEU 38 (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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34A CYS* 2.9 38.3 + - - +
37A TRP* 1.4 110.8 - - + +
39A ARG* 1.3 61.0 + - - +
40A PRO* 3.5 2.1 - - + -
43A HIS* 2.7 27.0 + - - -
48A ILE* 3.8 26.9 - - + +
51A LEU* 3.8 25.8 - - + +
52A VAL* 4.6 7.0 - - + -
49B LEU* 3.7 24.7 - - + -
52B VAL* 4.1 17.9 - - + -
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Residues in contact with ARG 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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5A PRO* 4.0 25.8 - - - +
8A PHE* 5.8 5.6 - - - -
35A ARG 2.9 13.1 + - - +
36A LEU* 3.5 21.5 + - - +
37A TRP 3.9 7.5 + - - +
38A LEU* 1.3 74.0 - - - +
40A PRO* 1.4 67.8 - - - +
41A GLU* 3.2 11.2 - - - +
42A THR* 3.1 18.2 + - + +
43A HIS* 2.9 56.0 + - + +
51A LEU* 6.0 0.6 - - - +
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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
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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