Contacts of the strand formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU* 5.9 5.7 - - + +
5A CYS 2.9 16.3 + - - +
6A ARG* 3.3 47.1 + - + +
7A VAL* 2.6 34.3 + - - +
32A GLY 4.1 0.8 + - - -
33A PHE* 1.3 70.1 - - - +
35A VAL* 1.3 55.6 + - - +
36A ASP* 4.5 0.7 - - - +
17B GLY 5.5 0.5 + - - -
18B TYR* 2.4 43.4 + - - -
22B ARG* 4.6 2.9 + - - -
291B LEU 5.4 0.9 - - - +
292B ARG* 5.3 3.3 - - - -
293B MET 5.8 0.3 + - - -
294B VAL* 4.8 7.5 + - - +
295B GLN* 3.9 24.3 + - - +
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Residues in contact with VAL 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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7A VAL* 3.4 8.3 - - + +
9A SER* 4.4 14.1 - - - -
24A ALA 5.9 0.2 - - - -
25A THR* 4.0 32.1 - - + +
28A LEU* 3.5 38.8 - - + -
29A GLN* 4.3 11.6 + - + +
33A PHE* 3.5 11.3 + - + +
34A GLU* 1.3 79.3 + - - +
36A ASP* 1.3 73.4 + - - +
37A ALA* 4.4 2.7 - - + +
18B TYR* 4.7 3.1 + - - -
22B ARG* 2.8 33.1 + - - -
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Residues in contact with ASP 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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6A ARG* 2.8 30.6 + - - +
7A VAL 2.7 8.5 + - - +
8A LEU* 3.5 4.6 - - + +
9A SER 2.8 26.0 + - - +
34A GLU* 4.1 1.6 + - - +
35A VAL* 1.3 76.5 - - - +
37A ALA* 1.3 60.3 + - - +
77A TYR* 2.6 45.9 + - + +
15B VAL* 3.0 23.9 - - + +
16B ARG* 3.5 18.6 + - - +
17B GLY 4.7 0.2 + - - -
22B ARG* 4.2 3.1 + - - -
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Residues in contact with ALA 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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9A SER 3.4 3.6 - - - +
21A ASN* 3.6 23.1 - - + +
25A THR* 4.3 12.8 - - + +
35A VAL* 3.7 5.1 + - + -
36A ASP* 1.3 73.0 - - - +
38A VAL* 1.3 62.3 + - - +
39A ASN* 4.4 5.4 - - - +
13B HIS* 3.0 32.0 + - + -
15B VAL* 3.2 16.8 + - - +
22B ARG* 4.0 13.5 - - - +
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Residues in contact with VAL 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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8A LEU* 4.0 16.8 - - + -
9A SER 2.9 6.1 + - - -
10A ILE* 3.4 28.6 - - + -
11A GLN 3.1 15.6 + - - +
21A ASN* 3.0 12.3 - - - +
37A ALA* 1.3 73.8 - - - +
39A ASN* 1.3 67.7 + - - +
40A SER 3.5 0.2 + - - -
57A LEU* 4.4 4.7 - - + -
62A LEU* 4.0 19.1 - - + -
65A LEU* 4.1 22.7 - - + -
66A TYR* 6.2 0.7 - - - +
69A LEU* 5.5 2.5 - - + -
15B VAL* 3.4 28.5 - - + -
42B GLN* 3.7 3.4 - - - +
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Residues in contact with ASN 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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11A GLN 3.2 4.3 - - - -
13A HIS* 3.4 32.7 + - + +
21A ASN* 3.3 21.7 - - - +
37A ALA* 4.4 5.0 - - - +
38A VAL* 1.3 70.4 - - - +
40A SER* 1.3 65.7 + - - +
41A VAL* 3.1 8.3 + - - +
42A GLN* 5.6 2.0 - - + -
57A LEU* 3.5 9.6 - - - +
13B HIS* 3.5 24.8 + - - -
39B ASN* 3.3 28.5 - - - +
42B GLN* 2.7 30.4 - - - +
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Residues in contact with SER 40 (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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10A ILE* 4.8 0.7 - - - -
11A GLN* 2.9 30.2 + - - -
12A SER* 3.1 2.1 + - - -
38A VAL* 3.5 3.8 + - - +
39A ASN* 1.3 71.4 - - - +
41A VAL* 1.3 67.5 + - - +
56A VAL* 4.2 0.2 - - - +
57A LEU* 3.0 28.9 + - - +
84A TYR 5.0 0.4 + - - -
90A PHE* 3.6 35.9 - - - -
123A GLU* 3.0 25.1 + - - -
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Residues in contact with VAL 41 (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 SER* 3.3 29.8 - - - -
13A HIS* 3.0 25.8 + - - +
39A ASN* 3.1 8.2 - - - +
40A SER* 1.3 87.4 + - - +
42A GLN* 1.3 63.6 + - - +
43A PHE* 3.9 7.0 - - + -
55A GLN 3.5 11.2 - - - +
56A VAL* 3.6 30.5 - - + +
57A LEU* 4.4 1.6 - - - +
122A GLY 3.3 17.7 - - - +
123A GLU* 3.8 24.2 - - + +
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Residues in contact with GLN 42 (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 HIS* 3.2 26.9 - - + -
15A VAL* 4.6 2.1 - - + +
39A ASN* 5.6 1.8 - - + -
41A VAL* 1.3 76.7 - - - +
43A PHE* 1.3 63.0 + - - +
54A GLY* 3.1 4.5 - - - -
55A GLN* 3.0 31.6 + - + +
37B ALA 3.9 0.6 + - - -
38B VAL* 3.7 6.5 - - - +
39B ASN* 2.7 56.2 - - - +
57B LEU* 3.7 16.6 - - - +
65B LEU* 3.7 25.0 - - + +
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Residues in contact with PHE 43 (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 HIS 2.9 6.3 + - - -
14A VAL* 3.0 5.5 - - + -
15A VAL* 2.8 27.0 + - - +
41A VAL* 3.9 17.0 - - + -
42A GLN* 1.3 80.0 - - - +
44A SER* 1.3 59.5 + - - +
45A ASN 3.8 12.8 - - - +
52A TRP* 3.7 22.0 - + + -
53A LYS* 3.3 22.4 - - - -
54A GLY 3.7 20.0 - - - -
55A GLN 4.0 5.2 - - - -
56A VAL* 3.9 17.7 - - + -
122A GLY 3.4 23.3 - - - +
123A GLU 3.6 15.3 - - - -
124A GLY* 3.6 23.3 - - - -
65B LEU* 3.7 4.9 - - - -
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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