Contacts of the helix formed by residues 29 - 41 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 4.3 8.8 + - - +
27B LYS 4.0 0.8 + - - -
28B LEU* 1.3 79.8 - - - +
30B LYS* 1.3 60.9 + - - +
31B LYS* 3.7 7.7 + - - +
32B GLU* 3.1 36.1 + - - +
33B LEU* 2.7 27.8 + - - +
68B GLU* 5.0 10.3 - - - -
69B VAL* 5.8 1.6 - - - -
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Residues in contact with LYS 30 (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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29B SER* 1.3 72.7 - - - +
31B LYS* 1.3 58.7 + - - +
33B LEU* 3.4 10.4 - - - +
34B LYS* 2.8 31.4 + - - +
54B VAL* 4.9 12.8 - - + +
55B ASP* 3.7 24.5 + - - +
58B MET* 3.5 45.8 - - + -
67B GLY 4.3 6.7 - - - +
68B GLU* 5.8 2.0 - - - +
69B VAL* 5.3 5.3 - - + +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 6.5 1.1 - - - +
22B GLU* 2.5 44.1 + - - +
29B SER* 3.2 4.8 + - - +
30B LYS* 1.3 78.6 - - - +
32B GLU* 1.3 65.5 + - + +
34B LYS* 3.2 7.0 + - + +
35B GLU* 2.9 47.1 + - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS 3.9 7.9 - - - +
19B SER* 2.6 23.5 - - - +
21B LYS* 5.3 7.6 - - - +
22B GLU* 2.3 50.2 + - + +
27B LYS 3.7 1.6 - - - +
28B LEU* 3.4 14.7 - - + +
29B SER* 3.1 24.7 + - - +
31B LYS* 1.3 81.1 - - + +
33B LEU* 1.3 52.8 + - - +
35B GLU* 3.2 7.4 + - - +
36B LEU* 2.7 42.9 + - + +
101B CA 2.4 21.1 - - - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.3 13.6 - - + +
29B SER 2.7 16.9 + - - +
30B LYS* 3.4 9.6 - - - +
32B GLU* 1.3 77.5 - - - +
34B LYS* 1.3 62.3 + - - +
36B LEU* 3.2 2.3 + - + +
37B LEU* 3.0 40.6 + - + +
54B VAL* 5.5 7.0 - - + +
57B VAL* 4.9 3.8 - - + -
58B MET* 4.5 18.8 - - + +
61B LEU* 3.6 24.7 - - + -
69B VAL* 4.6 10.3 - - + -
74B TYR* 3.2 42.4 - - + -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS 2.8 18.1 + - - +
31B LYS* 3.4 8.3 - - + +
33B LEU* 1.3 77.0 - - - +
35B GLU* 1.3 59.7 + - - +
37B LEU* 4.3 3.5 - - + +
38B GLN* 2.4 78.4 + - + +
47B ALA* 4.1 16.2 - - + -
48B GLN* 5.4 1.5 - - - +
51B VAL* 5.6 12.8 - - - +
54B VAL* 3.6 38.6 - - + -
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Residues in contact with GLU 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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21B LYS* 4.6 17.3 - - - +
31B LYS* 2.9 38.6 + - + +
32B GLU* 3.6 7.4 - - - +
34B LYS* 1.3 82.9 + - + +
36B LEU* 1.3 60.2 + - + +
38B GLN* 4.2 15.9 - - - +
39B THR* 2.7 43.3 + - + +
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Residues in contact with LEU 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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14B VAL* 5.6 0.9 - - + -
15B PHE* 5.0 10.3 - - + -
18B HIS* 3.0 56.5 - - + +
19B SER* 5.0 1.3 - - - +
21B LYS* 5.4 1.8 - - - +
28B LEU* 4.0 31.2 - - + -
32B GLU* 2.7 27.3 + - + +
33B LEU* 3.8 4.5 - - - +
35B GLU* 1.3 73.6 - - - +
37B LEU* 1.3 59.8 + - + +
39B THR* 4.1 1.8 - - + -
40B GLU* 2.8 48.6 + - - +
74B TYR* 4.4 17.7 - - + +
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Residues in contact with LEU 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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4A LEU* 5.6 0.2 - - + -
33B LEU* 3.0 34.7 + - + +
34B LYS* 4.3 2.9 - - + +
36B LEU* 1.3 75.9 - - - +
38B GLN* 1.3 57.6 + - - +
41B LEU* 2.8 44.6 + - + +
45B LEU* 3.6 34.5 - - + +
47B ALA* 6.1 4.3 - - + -
57B VAL* 4.4 20.9 - - + -
74B TYR* 3.1 34.5 - - + +
77B LEU* 5.7 0.9 - - + -
78B VAL* 5.7 1.6 - - + -
81B LEU* 4.7 10.1 - - + -
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Residues in contact with GLN 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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34B LYS* 2.4 63.4 + - + +
35B GLU* 4.1 13.9 - - - +
37B LEU* 1.3 80.1 - - - +
39B THR* 1.3 50.2 + - - +
41B LEU 4.8 0.4 - - - -
42B SER* 2.3 41.0 + - - +
46B ASP* 6.2 0.7 - - - -
47B ALA* 5.2 12.7 - - + +
48B GLN* 3.4 39.3 - - + +
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Residues in contact with THR 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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1A GLY 5.3 5.0 + - - -
2A SER* 5.0 3.9 - - - -
18B HIS* 5.1 11.9 - - + -
35B GLU* 2.7 35.4 + - + +
36B LEU* 3.8 2.2 - - + +
38B GLN* 1.3 75.1 - - - +
40B GLU* 1.3 89.8 + - + +
42B SER* 3.0 14.6 + - - -
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Residues in contact with GLU 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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1A GLY 5.0 1.7 + - - -
2A SER* 3.1 33.7 + - - +
4A LEU* 2.7 42.1 - - + +
5A GLU* 4.0 18.9 - - - +
14B VAL* 3.8 12.8 - - - +
18B HIS* 3.1 32.7 + - - +
36B LEU* 2.8 31.3 + - - +
39B THR* 1.3 90.6 - - + +
41B LEU* 1.3 73.0 + - + +
42B SER 3.6 0.6 + - - -
44B PHE* 6.0 0.2 - - - -
74B TYR* 4.7 0.5 + - - -
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Residues in contact with LEU 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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4A LEU* 3.5 23.1 - - + -
5A GLU* 5.3 1.1 - - + +
8A MET* 3.5 37.0 - - + -
36B LEU 4.5 1.6 - - - +
37B LEU* 2.8 28.5 + - + +
40B GLU* 1.3 95.3 - - + +
42B SER* 1.3 59.7 + - - +
43B GLY 3.0 4.3 - - - +
44B PHE* 4.1 11.0 - - + +
45B LEU* 2.8 64.7 + - + +
46B ASP 3.3 0.7 + - - -
78B VAL* 5.9 2.9 - - + -
81B LEU* 5.1 5.8 - - + +
85B CYS* 5.8 0.2 - - + -
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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