Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 3LRA
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 GLN 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU 6.1 1.1 - - - -
27A ASP 2.7 2.4 - - - +
28A ARG* 1.3 88.8 - - + +
30A LEU* 1.3 57.6 + - - +
31A ARG 2.9 1.3 - - - -
32A SER* 3.7 4.7 - - - -
33A SER* 2.6 41.2 + - - -
89A GLN* 6.0 2.4 - - - +
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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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22A LEU* 3.9 18.6 - - + -
26A GLU* 3.9 23.0 + - - +
27A ASP* 3.8 4.4 + - - +
29A GLN* 1.3 78.6 - - - +
31A ARG* 1.3 56.8 + - - +
33A SER* 3.8 3.4 - - - -
34A ILE* 2.8 52.3 + - + +
86A LEU* 4.3 5.4 - - + -
89A GLN* 3.2 59.7 - - + +
90A LEU* 4.2 9.9 - - + -
93A HIS* 4.0 17.0 - - + +
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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
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19A ARG* 2.6 81.4 + - + +
20A SER* 4.3 5.7 - - - +
22A LEU* 3.6 26.1 + - + -
23A SER* 3.4 16.8 + - - +
27A ASP* 2.9 51.0 + - + +
29A GLN 2.9 0.6 - - - -
30A LEU* 1.3 75.1 - - - +
32A SER* 1.3 51.3 + - - +
33A SER 2.7 14.4 + - - -
34A ILE* 4.1 4.0 - - - +
35A GLU* 2.8 16.1 + - - +
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Residues in contact with SER 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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19A ARG* 4.5 3.1 - - - +
27A ASP 3.8 1.4 + - - -
28A ARG 3.3 23.8 - - - -
29A GLN* 3.1 5.6 + - - -
31A ARG* 1.3 78.1 - - - +
33A SER* 1.3 58.6 + - - +
35A GLU* 3.9 9.8 - - - +
36A ARG* 3.5 35.3 + - - +
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Residues in contact with SER 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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29A GLN* 2.6 20.8 + - - -
30A LEU* 3.8 6.3 - - - -
31A ARG 2.7 0.2 + - - -
32A SER* 1.3 77.2 - - - +
34A ILE* 1.3 62.7 + - - -
35A GLU 2.9 6.0 + - - -
36A ARG* 3.0 24.5 + - - +
37A VAL* 3.6 8.3 + - - +
82A LEU* 3.1 30.4 - - - +
86A LEU* 4.2 15.1 - - - +
89A GLN* 4.7 3.8 + - - -
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Residues in contact with ILE 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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15A LEU* 3.3 45.3 - - + +
18A TYR 4.6 2.2 - - - +
19A ARG* 3.9 26.5 - - + -
22A LEU* 4.7 1.6 - - + -
30A LEU* 2.8 40.1 + - + +
31A ARG* 2.9 6.5 + - - +
33A SER* 1.3 75.0 - - - +
35A GLU* 1.3 53.5 + - - +
37A VAL* 3.7 8.0 + - - +
38A ILE* 2.7 37.8 + - + +
86A LEU* 4.4 9.4 - - + -
90A LEU* 3.3 32.8 - - + -
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Residues in contact with GLU 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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19A ARG* 3.6 29.1 + - - +
31A ARG 2.8 14.9 + - - +
32A SER* 3.9 10.3 - - - +
33A SER 2.9 0.2 - - - -
34A ILE* 1.3 77.0 - - - +
36A ARG* 1.3 70.0 + - - +
38A ILE* 2.9 25.2 + - - +
39A ASN* 2.8 24.2 + - + +
42A GLN* 5.0 0.6 - - - +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A SER* 3.5 27.0 + - - +
33A SER* 3.4 15.3 - - - +
35A GLU* 1.3 78.4 - - - +
37A VAL* 1.3 60.4 + - + +
39A ASN* 3.3 6.1 - - - +
40A ILE* 2.8 42.7 + - + +
82A LEU* 4.3 24.7 - - + -
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Residues in contact with VAL 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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15A LEU* 3.3 28.3 - - + -
33A SER* 3.6 9.8 + - - +
34A ILE 3.9 2.7 - - - +
35A GLU 3.1 0.4 - - - -
36A ARG* 1.3 75.8 - - + +
38A ILE* 1.3 56.6 + - - +
40A ILE* 4.3 8.7 - - + -
41A PHE* 2.8 66.9 + - + -
82A LEU* 5.4 7.0 - - + -
83A LEU* 3.5 30.5 - - + +
86A LEU* 4.0 17.0 - - + -
107A PHE* 4.2 1.8 - - + -
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Residues in contact with ILE 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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12A LEU* 3.7 11.2 - - + +
15A LEU* 3.8 16.8 - - + +
16A GLU* 3.3 64.2 - - + +
19A ARG* 4.9 6.7 - - - -
34A ILE* 2.7 28.5 + - + +
35A GLU* 2.9 21.0 + - - +
37A VAL* 1.3 75.9 - - - +
39A ASN* 1.3 65.5 + - - +
41A PHE* 3.0 2.4 + - - +
42A GLN* 2.9 37.0 + - - +
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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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35A GLU* 2.8 22.5 + - + +
36A ARG* 3.3 11.2 - - - +
38A ILE* 1.3 72.4 - - - +
40A ILE* 1.3 71.8 + - - +
42A GLN* 3.1 16.1 + - - +
43A SER* 2.8 24.0 + - - -
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Residues in contact with ILE 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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36A ARG* 2.8 31.6 + - + +
37A VAL* 3.7 7.9 - - + +
39A ASN* 1.3 78.4 - - - +
41A PHE* 1.3 65.9 + - + +
43A SER* 3.1 12.8 - - - -
46A PHE* 2.9 45.1 - - + +
79A LEU* 3.8 15.3 - - + -
82A LEU* 6.4 0.2 - - + -
116A VAL* 4.1 11.2 - - + -
119A HIS* 3.7 21.5 - - + +
120A GLU* 3.0 36.1 - - - +
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Residues in contact with PHE 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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8A THR* 3.4 45.8 - - + -
11A ALA* 4.5 3.8 - - + -
12A LEU* 3.3 26.7 - - + -
15A LEU* 5.9 0.9 - - + -
37A VAL* 2.8 52.4 + - + +
40A ILE* 1.3 79.5 - - + +
42A GLN* 1.3 59.7 + - - +
43A SER 3.9 3.3 - - - +
46A PHE* 3.4 37.8 - + - +
47A GLN* 4.6 4.5 + - - +
50A ILE* 5.5 0.2 - - - +
83A LEU* 4.9 0.4 - - + -
107A PHE* 3.7 28.5 - + - -
112A LEU* 4.1 17.5 - - + -
116A VAL* 4.7 10.5 - - + -
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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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12A LEU* 4.4 11.6 - - + +
16A GLU* 3.4 21.0 + - - -
35A GLU* 5.0 1.0 - - - +
38A ILE* 2.9 37.3 + - - +
39A ASN* 3.3 16.9 - - - +
41A PHE* 1.3 69.6 - - - +
43A SER* 1.3 69.4 + - - +
44A ASN* 3.5 4.9 + - - -
47A GLN* 5.1 4.7 - - - +
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Residues in contact with SER 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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39A ASN* 2.8 14.5 + - - -
40A ILE* 3.1 18.8 + - - -
41A PHE 3.9 0.2 - - - +
42A GLN* 1.3 82.1 - - - +
44A ASN* 1.3 65.6 + - - +
45A LEU* 3.4 6.8 + - - +
46A PHE* 3.8 1.3 - - - +
47A GLN* 3.3 19.6 + - - +
119A HIS* 3.3 27.7 - - - -
123A HIS* 5.4 3.6 + - - -
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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