Contacts of the strand formed by residues 34 - 43 (chain B) in PDB entry 1LHR
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 GLU 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY 5.6 0.2 + - - -
18A TYR* 2.4 43.8 + - - -
22A ARG* 4.6 2.6 + - - -
291A LEU 5.3 1.6 - - - +
292A ARG* 5.3 4.0 - - - -
293A MET 5.6 0.3 + - - -
294A VAL* 4.6 5.7 + - - +
295A GLN* 3.9 25.1 + - - +
5B CYS 2.9 16.0 + - - +
6B ARG* 3.2 45.6 + - + +
7B VAL* 2.8 32.9 + - - +
32B GLY 3.9 1.2 + - - -
33B PHE* 1.3 70.9 - - - +
35B VAL* 1.3 54.8 + - - +
36B ASP* 4.5 0.9 - - - +
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Residues in contact with VAL 35 (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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18A TYR* 4.7 2.5 + - - -
22A ARG* 2.7 39.5 + - - -
7B VAL* 3.5 10.3 - - + +
9B SER* 4.3 16.8 - - - -
25B THR* 4.3 28.7 - - + +
28B LEU* 3.6 36.8 - - + -
29B GLN* 4.1 13.6 + - + +
33B PHE* 3.5 11.8 + - + +
34B GLU* 1.3 76.1 + - - +
36B ASP* 1.3 67.4 + - - +
37B ALA* 4.6 2.2 - - + +
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Residues in contact with ASP 36 (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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15A VAL* 3.1 23.6 - - + +
16A ARG* 3.4 20.7 + - - +
22A ARG* 4.3 2.3 + - - -
6B ARG* 3.0 30.2 + - - +
7B VAL 2.7 11.0 + - - +
8B LEU* 3.6 4.5 - - + +
9B SER 3.0 25.1 + - - -
34B GLU* 4.5 1.6 - - - +
35B VAL* 1.3 77.3 - - - +
37B ALA* 1.3 59.6 + - - +
77B TYR* 2.6 41.9 + - + +
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Residues in contact with ALA 37 (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 HIS* 2.8 36.8 + - + +
15A VAL* 3.1 16.8 + - - +
22A ARG* 3.7 14.2 - - - +
9B SER 3.5 3.8 - - - +
21B ASN* 3.8 20.9 - - + +
25B THR* 4.4 13.5 - - + +
35B VAL* 4.7 4.7 - - + -
36B ASP* 1.3 72.4 - - - +
38B VAL* 1.3 63.1 + - - +
39B ASN* 4.5 2.9 - - - +
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Residues in contact with VAL 38 (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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15A VAL* 3.8 27.6 - - + -
42A GLN* 3.8 3.6 - - - +
8B LEU* 4.0 16.8 - - + -
9B SER 2.9 4.9 + - - -
10B ILE* 4.0 22.0 - - + -
11B GLN 3.2 14.9 + - - +
21B ASN* 2.9 13.4 - - - +
36B ASP 4.0 0.4 + - - -
37B ALA* 1.3 72.2 - - - +
39B ASN* 1.3 66.4 + - - +
40B SER* 3.5 1.1 + - - +
57B LEU* 4.8 3.1 - - + -
62B LEU* 3.8 28.3 - - + -
65B LEU* 4.3 20.4 - - + -
69B LEU* 5.6 2.7 - - + -
90B PHE* 5.3 0.4 - - + -
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Residues in contact with ASN 39 (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 HIS* 3.3 29.0 + - - -
39A ASN* 3.3 27.7 - - - +
42A GLN* 2.7 31.0 - - - +
11B GLN 3.3 4.0 - - - -
13B HIS* 3.4 22.3 + - + +
21B ASN* 3.4 20.4 - - - +
37B ALA* 4.5 3.3 - - - +
38B VAL* 1.3 73.1 - - - +
40B SER* 1.3 64.7 + - - +
41B VAL* 3.1 16.7 + - - +
42B GLN* 5.7 1.8 - - + -
57B LEU* 3.6 10.4 - - - +
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Residues in contact with SER 40 (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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10B ILE* 4.8 1.1 - - - -
11B GLN* 2.9 30.9 + - - -
12B SER* 3.1 8.3 + - - -
38B VAL* 3.5 3.6 + - - -
39B ASN* 1.3 71.3 - - - +
41B VAL* 1.3 71.0 + - - +
57B LEU* 3.0 28.6 + - - +
84B TYR 4.8 6.8 + - - -
85B THR* 6.6 0.2 - - - -
90B PHE* 3.6 37.5 - - - -
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Residues in contact with VAL 41 (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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12B SER* 3.4 27.3 - - - +
13B HIS* 3.1 27.7 + - - +
39B ASN* 3.1 8.2 - - - +
40B SER* 1.3 93.0 + - - +
42B GLN* 1.3 62.7 + - - +
43B PHE* 3.3 26.7 - - + -
55B GLN 3.3 13.2 - - - +
56B VAL* 3.9 23.6 - - + +
57B LEU* 4.5 4.3 - - - +
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Residues in contact with GLN 42 (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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37A ALA 4.0 0.6 + - - -
38A VAL* 3.7 10.5 - - - +
39A ASN* 2.7 53.6 - - - +
57A LEU* 4.1 6.4 - - - +
65A LEU* 3.6 27.3 - - + +
13B HIS* 3.3 26.3 + - + -
15B VAL* 4.4 2.3 - - + +
39B ASN* 5.7 2.0 - - + -
41B VAL* 1.3 75.4 - - - +
43B PHE* 1.3 64.3 + - - +
54B GLY* 3.0 4.0 - - - -
55B GLN* 2.9 42.5 + - + +
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Residues in contact with PHE 43 (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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65A LEU* 3.9 4.5 - - - -
13B HIS 3.0 7.6 + - - -
14B VAL* 3.2 9.1 - - + -
15B VAL* 2.9 28.1 + - - +
41B VAL* 3.3 44.2 - - + -
42B GLN* 1.3 74.4 - - - +
44B SER* 1.3 60.7 + - - +
45B ASN 3.4 16.8 - - - +
52B TRP* 3.8 26.2 - + - -
53B LYS 3.2 11.0 - - - +
54B GLY* 3.6 27.6 - - - -
55B GLN 4.1 2.0 - - - -
56B VAL* 4.0 20.6 - - + -
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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