Contacts of the helix formed by residues 22 - 39 (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 GLY 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 4.5 7.2 + - - -
20B SER* 3.2 7.9 + - - -
21B PRO* 1.3 79.7 - - - +
23B PRO* 1.3 75.0 - - - +
24B ARG 3.3 2.2 - - - -
25B GLU* 3.2 13.8 + - - -
26B ALA* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.8 8.1 - - + -
81A VAL* 3.9 17.5 - - + +
84A LEU* 3.8 30.5 - - + -
85A GLU* 4.9 9.9 - - + +
88A GLU* 5.6 5.8 - - - +
17B TYR* 3.6 30.2 - - + +
22B GLY* 1.3 82.2 - - - +
24B ARG* 1.3 65.4 + - - +
25B GLU* 4.8 0.2 - - - +
26B ALA* 3.2 2.0 + - + +
27B VAL* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.7 35.4 + - - +
81A VAL* 3.2 38.9 - - + +
82A THR* 3.6 19.8 + - - -
85A GLU* 3.6 24.0 + - - +
22B GLY 3.3 0.4 - - - -
23B PRO* 1.3 83.5 - - - +
25B GLU* 1.3 69.6 + - - +
27B VAL* 3.5 2.6 + - + +
28B SER* 3.1 22.2 + - - -
31B ARG* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 3.9 3.8 - - - -
21B PRO* 3.8 35.7 - - + +
22B GLY* 3.3 28.7 - - - +
23B PRO* 4.8 0.3 - - - +
24B ARG* 1.3 81.1 + - + +
26B ALA* 1.3 67.1 + - - +
28B SER* 3.2 8.0 + - - -
29B GLN* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.1 17.3 - - + -
60A ILE* 5.1 0.9 - - + -
15B PHE* 4.0 19.4 - - + -
17B TYR* 4.2 15.9 - - + +
20B SER* 3.2 18.1 + - - +
22B GLY 3.0 9.8 + - - +
23B PRO* 3.6 7.2 - - + +
25B GLU* 1.3 75.9 - - - +
27B VAL* 1.3 64.1 + - - +
29B GLN* 3.3 2.6 + - - +
30B LEU* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.2 7.1 - - + +
57A PHE* 3.6 34.1 - - + -
77A GLY* 4.1 14.8 - - - +
78A GLU* 4.4 4.0 - - - +
81A VAL* 3.5 28.0 - - + -
23B PRO 2.9 11.0 + - - +
24B ARG* 3.9 4.0 - - + +
26B ALA* 1.3 78.3 - - - +
28B SER* 1.3 63.0 + - - +
30B LEU* 3.4 7.2 + - - +
31B ARG* 3.0 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG 3.1 14.4 + - - -
25B GLU* 3.2 11.2 + - - -
27B VAL* 1.3 77.6 - - - +
29B GLN* 1.3 62.7 + - - +
31B ARG* 3.3 19.7 + - - +
32B GLU* 3.1 24.0 + - - +
35B ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 5.1 6.3 - - - +
15B PHE* 3.2 41.0 - - + -
20B SER* 5.5 1.8 - - - -
25B GLU 2.9 20.0 + - - +
26B ALA 3.8 0.2 - - - +
28B SER* 1.3 71.1 + - - +
30B LEU* 1.3 60.5 + - - +
32B GLU* 3.2 25.5 + - - +
33B LEU* 2.8 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.1 14.1 - - + +
56A GLN* 3.9 14.1 - - + -
57A PHE* 3.6 44.4 - - + +
60A ILE* 3.8 14.4 - - + -
12B PHE* 3.7 31.6 - - + +
15B PHE* 3.7 25.6 - - + +
26B ALA 3.0 21.3 + - - +
27B VAL* 3.7 4.9 - - - +
29B GLN* 1.3 71.6 - - - +
31B ARG* 1.3 61.2 + - - +
33B LEU* 3.3 3.7 + - + +
34B CYS* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 2.5 39.4 + - - +
53A VAL* 3.9 17.2 - - + +
78A GLU* 2.5 39.5 + - - +
97A EMC 3.9 9.6 - - + +
27B VAL* 3.0 35.8 + - - +
28B SER* 3.5 21.5 - - - +
29B GLN 3.3 0.2 - - - -
30B LEU* 1.3 76.2 - - - +
32B GLU* 1.3 56.3 + - - +
34B CYS* 3.4 2.1 + - - +
35B ARG* 3.0 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.1 12.0 + - - +
29B GLN* 3.2 28.0 + - - +
31B ARG* 1.3 79.1 - - - +
33B LEU* 1.3 66.3 + - + +
35B ARG* 3.4 15.6 + - - +
36B LEU* 3.2 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.5 3.9 - - + +
11B ARG* 3.8 44.9 - - + +
12B PHE* 3.8 21.6 - - + +
15B PHE* 3.8 40.6 - - + -
29B GLN* 2.8 37.6 + - + +
30B LEU* 3.8 6.3 - - + +
32B GLU* 1.3 73.1 - - + +
34B CYS* 1.3 63.6 + - - +
36B LEU* 3.2 27.2 + - + +
37B TRP* 3.3 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.0 16.4 - - - -
52A VAL* 4.0 11.0 - - - -
53A VAL* 3.8 19.3 - - + -
97A EMC 4.9 1.8 - - - -
12B PHE* 3.7 24.4 - - + -
30B LEU 2.8 22.1 + - - +
31B ARG 3.7 4.3 - - - +
33B LEU* 1.3 74.5 - - - +
35B ARG* 1.3 57.8 + - - +
37B TRP* 3.2 5.4 + - - +
38B LEU* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 5.5 1.5 - - + +
97A EMC 3.6 30.2 - - + +
28B SER 5.5 0.2 + - - -
31B ARG* 3.0 46.0 + - - +
32B GLU* 3.4 12.4 + - - +
34B CYS* 1.3 75.5 - - - +
36B LEU* 1.3 58.8 + - + +
39B ARG* 2.9 29.1 + - - +
40B PRO* 3.7 27.3 - - + +
41B GLU* 4.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.4 55.4 - - + -
11B ARG* 6.2 1.3 - - - +
32B GLU* 3.2 25.9 + - + +
33B LEU* 3.2 22.6 + - + +
34B CYS 3.2 1.2 - - - -
35B ARG* 1.3 78.7 - - + +
37B TRP* 1.3 58.1 + - - +
39B ARG* 3.8 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.8 2.5 - - + -
5B PRO* 3.7 31.0 + - + +
8B PHE* 3.7 15.8 - - + +
9B ARG* 3.4 37.1 - - + +
12B PHE* 3.8 25.4 - + + -
13B ARG* 3.9 17.5 - - - -
33B LEU 3.3 8.2 + - - +
34B CYS* 3.2 6.1 + - - +
36B LEU* 1.3 79.0 - - - +
38B LEU* 1.3 97.0 + - + +
39B ARG* 3.5 10.9 + - - -
43B HIS* 4.8 1.4 - - - -
51B LEU* 4.0 37.0 - - + +
52B VAL* 4.7 7.2 - - + -
55B GLU* 3.2 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.4 35.0 - - + -
52A VAL* 4.2 15.7 - - + -
34B CYS* 2.9 29.2 + - - +
37B TRP* 1.3 110.9 - - + +
39B ARG* 1.3 62.6 + - - +
40B PRO* 3.4 2.8 - - + -
43B HIS* 2.8 28.6 + - - +
48B ILE* 3.8 25.4 - - + +
51B LEU* 3.9 26.0 - - + +
52B VAL* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.1 23.9 - - - +
8B PHE* 5.8 3.4 - - - -
35B ARG 2.9 12.5 + - - +
36B LEU* 3.8 21.8 - - - +
37B TRP 4.0 7.7 + - - -
38B LEU* 1.3 77.5 - - - +
40B PRO* 1.3 64.4 - - - +
41B GLU* 3.1 23.5 + - - +
42B THR* 2.9 28.6 + - - +
43B HIS* 2.8 52.1 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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