Contacts of the helix formed by residues 29 - 41 (chain A) in PDB entry 2LP3
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 SER 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 4.3 8.6 + - - +
27A LYS 4.0 1.3 + - - -
28A LEU* 1.3 78.8 - - - +
30A LYS* 1.3 59.3 + - - +
31A LYS* 3.7 7.1 + - - +
32A GLU* 3.1 35.3 + - - +
33A LEU* 2.7 28.3 + - - +
68A GLU* 5.0 11.0 - - - -
69A VAL* 5.8 1.6 - - - -
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Residues in contact with LYS 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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29A SER* 1.3 73.1 - - - +
31A LYS* 1.3 58.5 + - - +
33A LEU* 3.2 10.3 + - - +
34A LYS* 2.8 31.6 + - - +
54A VAL* 4.9 12.8 - - + +
55A ASP* 3.7 24.7 + - - +
58A MET* 3.5 46.9 - - + -
67A GLY 4.3 6.3 - - - +
68A GLU* 5.8 2.2 - - - +
69A VAL* 5.3 4.4 - - + +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 6.5 0.9 - - - +
22A GLU* 2.5 43.7 + - - +
29A SER* 3.2 4.9 + - - +
30A LYS* 1.3 78.9 - - - +
32A GLU* 1.3 66.8 + - + +
34A LYS* 3.2 6.6 + - + +
35A GLU* 2.9 46.6 + - + +
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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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18A HIS 3.9 8.3 - - - +
19A SER* 2.6 22.4 - - - +
21A LYS* 5.3 7.2 - - - +
22A GLU* 2.3 49.1 + - + +
27A LYS 3.7 1.4 - - - +
28A LEU* 3.4 14.9 - - + +
29A SER* 3.1 24.5 + - - +
31A LYS* 1.3 81.6 - - + +
33A LEU* 1.3 52.6 + - - +
35A GLU* 3.2 6.7 + - - +
36A LEU* 2.7 43.5 + - + +
201A CA 2.4 22.1 - - - -
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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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28A LEU* 3.3 12.3 - - + +
29A SER 2.7 16.4 + - - +
30A LYS* 3.4 9.0 - - - +
32A GLU* 1.3 77.1 - - - +
34A LYS* 1.3 63.7 + - - +
36A LEU* 3.2 3.2 + - + +
37A LEU* 3.0 41.5 + - + +
54A VAL* 5.5 7.4 - - + +
57A VAL* 4.9 4.3 - - + -
58A MET* 4.5 18.4 - - + +
61A LEU* 3.6 24.9 - - + -
69A VAL* 4.6 10.3 - - + -
74A TYR* 3.2 42.2 - - + -
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Residues in contact with LYS 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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30A LYS 2.8 17.5 + - - +
31A LYS* 3.4 8.5 - - + +
33A LEU* 1.3 77.0 - - - +
35A GLU* 1.3 61.3 + - - +
37A LEU* 5.1 3.1 - - + -
38A GLN* 2.4 78.9 + - + +
47A ALA* 4.1 16.4 - - + -
48A GLN* 5.9 0.9 - - - +
51A VAL* 5.6 12.6 - - - +
54A VAL* 3.6 39.7 - - + +
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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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21A LYS* 4.6 17.9 - - - +
31A LYS* 2.9 37.4 + - + +
32A GLU* 3.6 7.0 - - - +
34A LYS* 1.3 83.5 + - + +
36A LEU* 1.3 60.4 + - + +
38A GLN* 4.2 16.3 + - - +
39A THR* 2.7 43.4 + - + +
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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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14A VAL* 5.6 1.1 - - + -
15A PHE* 5.0 9.4 - - + -
18A HIS* 3.0 56.8 - - + +
19A SER* 5.0 1.1 - - - +
21A LYS* 5.4 1.6 - - - +
28A LEU* 4.0 31.6 - - + -
32A GLU* 2.7 26.1 + - + +
33A LEU* 3.8 4.3 - - - +
35A GLU* 1.3 74.4 - - + +
37A LEU* 1.3 60.3 + - + +
39A THR* 4.1 2.2 - - + -
40A GLU* 2.8 47.7 + - - +
41A LEU* 4.5 0.2 - - - +
74A TYR* 4.4 18.2 - - + +
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Residues in contact with LEU 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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33A LEU* 3.0 34.2 + - + +
34A LYS* 4.3 3.4 - - + +
36A LEU* 1.3 75.8 - - - +
38A GLN* 1.3 58.5 + - - +
41A LEU* 2.8 44.6 + - + +
45A LEU* 3.6 34.0 - - + +
57A VAL* 4.4 20.4 - - + -
74A TYR* 3.1 34.3 - - + +
77A LEU* 5.7 1.1 - - + -
78A VAL* 5.7 1.6 - - + -
81A LEU* 4.7 10.3 - - + -
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Residues in contact with GLN 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 LYS* 2.4 62.6 + - + +
35A GLU* 4.1 13.7 - - - +
37A LEU* 1.3 78.6 - - - +
39A THR* 1.3 48.9 + - - +
41A LEU 4.8 0.4 - - - -
42A SER* 2.3 41.2 + - - +
45A LEU* 5.7 0.4 - - - -
46A ASP* 6.2 0.2 - - - -
47A ALA* 5.2 12.3 - - + +
48A GLN* 3.4 39.3 - - + +
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Residues in contact with THR 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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18A HIS* 5.1 12.3 - - + +
21A LYS* 6.1 1.8 - - - +
35A GLU* 2.7 36.7 + - + +
36A LEU* 3.8 2.0 - - + +
38A GLN* 1.3 75.1 - - - +
40A GLU* 1.3 91.5 + - + +
42A SER* 3.0 14.5 + - - -
1B GLY 5.3 4.7 + - - -
2B SER* 5.0 3.5 - - - -
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Residues in contact with GLU 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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14A VAL* 3.8 13.4 - - - +
18A HIS* 3.1 33.2 + - - +
36A LEU* 2.8 31.7 + - - +
39A THR* 1.3 90.6 - - + +
41A LEU* 1.3 71.6 + - + +
42A SER 3.6 1.0 + - - -
74A TYR* 4.7 0.5 + - - -
1B GLY 5.0 1.6 + - - -
2B SER* 3.1 33.7 + - - +
4B LEU* 2.7 42.4 - - + +
5B GLU* 4.0 19.6 - - - +
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Residues in contact with LEU 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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36A LEU 4.5 1.3 - - - +
37A LEU* 2.8 29.7 + - + +
40A GLU* 1.3 94.0 - - + +
42A SER* 1.3 59.5 + - - +
43A GLY 3.0 3.8 - - - +
44A PHE* 4.1 10.8 - - + +
45A LEU* 2.8 64.8 + - + +
46A ASP 3.3 0.9 + - - -
78A VAL* 5.9 2.9 - - + -
81A LEU* 5.1 5.4 - - + +
4B LEU* 3.5 24.5 - - + -
5B GLU 5.3 0.7 - - - +
8B MET* 3.5 38.1 - - + -
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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