Contacts of the helix formed by residues 43 - 56 (chain A) in PDB entry 2LWP
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 VAL 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR* 3.7 27.0 + - + +
35A PRO 4.9 2.9 - - - +
36A GLN* 4.7 5.4 - - + +
37A GLN* 3.2 29.6 - - + +
42A PRO* 1.3 74.6 - - - +
44A VAL* 1.3 58.4 + - + +
45A GLN* 3.0 32.1 - - + +
46A ASP* 2.8 25.5 + - - +
78A LEU* 3.3 11.0 - - + -
81A LEU* 2.9 14.2 - - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 1.3 72.1 - - + +
45A GLN* 1.3 69.0 + - + +
47A LEU* 3.2 26.5 - - - +
72A LYS 3.6 4.0 - - - +
73A GLU 3.4 13.7 - - - +
74A MET* 3.4 30.3 - - + -
75A GLU 3.6 12.9 + - - +
76A THR 3.7 17.9 - - - +
77A PRO 4.9 0.2 - - - -
78A LEU* 3.5 29.2 - - + +
81A LEU* 3.5 8.3 - - - -
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 5.2 3.1 - - + -
43A VAL* 3.4 18.2 - - + -
44A VAL* 1.3 84.3 - - + +
46A ASP* 1.3 51.1 + - - +
48A ALA* 3.1 8.5 + - - +
49A GLN* 2.8 41.1 + - + +
72A LYS 4.3 2.7 - - - -
73A GLU* 3.0 41.4 + - - +
74A MET* 4.4 6.2 - - - +
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Residues in contact with ASP 46 (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 VAL* 3.1 12.2 - - - +
34A THR* 2.8 45.2 + - - +
42A PRO* 3.3 19.8 - - + +
43A VAL* 2.8 17.7 + - - +
45A GLN* 1.3 77.4 - - - +
47A LEU* 1.3 55.4 + - - +
49A GLN* 3.6 1.3 - - - -
50A LEU* 2.7 46.3 + - - +
67A LYS* 2.7 32.7 + - - -
81A LEU* 3.3 4.3 - - + +
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Residues in contact with LEU 47 (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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44A VAL 3.2 18.2 - - - +
46A ASP* 1.3 82.0 + - - +
48A ALA* 1.3 78.2 + - - +
51A VAL 3.7 7.8 + - - -
64A LEU* 3.1 30.7 - - + +
67A LYS* 3.8 16.4 - - - +
69A LYS* 3.4 44.4 - - + -
70A SER 3.1 24.0 - - - +
71A LEU* 3.4 8.3 - - - -
72A LYS 3.5 8.5 - - - +
75A GLU* 4.0 7.2 - - + -
76A THR* 3.9 5.8 - - - +
81A LEU* 3.4 18.1 - - + +
89A VAL* 3.7 4.5 - - - +
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Residues in contact with ALA 48 (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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45A GLN* 3.1 4.6 + - - +
47A LEU* 1.3 80.0 - - - +
49A GLN* 1.3 55.7 + - - +
51A VAL* 3.4 4.3 + - - +
52A GLU* 2.8 38.5 + - - +
59A LEU* 3.5 21.6 - - + +
71A LEU* 3.3 26.7 - - + -
72A LYS 3.2 25.8 - - - +
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Residues in contact with GLN 49 (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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31A LEU* 4.8 4.7 - - + -
32A LEU 5.2 1.8 - - - +
34A THR* 3.6 23.1 + - + +
45A GLN* 2.8 23.9 + - + +
46A ASP* 3.2 10.8 - - - +
48A ALA* 1.3 78.1 - - - +
50A LEU* 1.3 58.2 + - + +
52A GLU* 3.5 22.2 + - - -
53A GLU* 2.6 72.3 + - + +
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Residues in contact with LEU 50 (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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20A VAL* 3.2 39.9 - - + -
22A VAL* 3.4 2.6 - - - +
31A LEU* 2.9 30.1 - - + +
32A LEU 3.0 33.9 - - - +
33A VAL* 3.8 1.3 - - + +
34A THR* 5.0 0.9 - - - +
46A ASP* 2.7 52.6 + - - +
47A LEU 4.1 0.7 - - - +
49A GLN* 1.3 74.5 - - + +
51A VAL* 1.3 62.0 + - - +
54A ALA* 3.0 12.5 + - - +
67A LYS* 3.4 14.4 - - - +
86A GLY 3.7 2.9 - - - +
89A VAL* 3.2 17.5 - - + -
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Residues in contact with VAL 51 (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 VAL* 3.3 7.5 - - + +
47A LEU 3.7 1.0 + - - -
48A ALA 3.4 5.7 + - - +
49A GLN 3.4 0.2 - - - -
50A LEU* 1.3 80.1 - - - +
52A GLU* 1.3 64.7 + - - +
54A ALA* 3.8 9.5 - - - +
55A THR* 3.9 6.2 + - - -
62A GLN* 3.1 38.4 - - + +
64A LEU* 3.3 48.2 - - + -
71A LEU* 4.8 0.4 - - + -
89A VAL 3.5 12.3 - - - +
91A LEU* 3.3 37.8 - - + +
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Residues in contact with GLU 52 (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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48A ALA 2.8 20.0 + - - +
49A GLN* 3.5 23.0 + - - +
51A VAL* 1.3 75.8 - - - +
53A GLU* 1.3 56.3 + - - +
54A ALA 3.3 0.7 + - - -
55A THR* 3.4 2.1 + - - -
56A GLY* 2.8 32.0 + - - -
57A VAL 2.9 23.6 + - - +
58A PRO* 3.9 3.5 - - - +
59A LEU* 3.3 35.8 + - + +
62A GLN* 3.2 20.2 - - - +
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Residues in contact with GLU 53 (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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31A LEU* 3.6 26.3 - - + +
32A LEU* 5.2 7.3 + - - +
49A GLN* 2.6 46.1 + - - +
52A GLU* 1.3 74.6 - - - +
54A ALA* 1.3 66.0 + - - +
55A THR 3.2 1.2 + - - -
56A GLY* 3.4 11.1 + - - +
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Residues in contact with ALA 54 (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 VAL* 3.4 23.3 - - + -
29A TYR* 3.3 48.4 - - + +
31A LEU* 3.2 13.6 - - + +
50A LEU 3.0 17.6 + - - +
51A VAL 3.8 3.8 - - - +
52A GLU 3.2 0.4 - - - -
53A GLU* 1.3 78.6 - - - +
55A THR* 1.3 58.1 + - - +
95A LYS* 4.1 4.7 - - - +
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Residues in contact with THR 55 (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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27A GLU* 4.9 1.6 - - - +
29A TYR* 3.4 30.1 - - + -
51A VAL 3.9 6.8 + - - -
52A GLU 3.4 0.4 + - - -
53A GLU 4.1 0.9 - - - -
54A ALA* 1.3 73.7 - - - +
56A GLY* 1.3 62.3 + - - +
57A VAL* 3.1 22.4 - - - +
95A LYS* 3.1 37.3 - - + +
96A SER 4.3 1.9 - - - +
97A ASN* 3.2 38.7 + - - +
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Residues in contact with GLY 56 (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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52A GLU* 2.8 11.8 + - - -
53A GLU* 3.4 11.1 + - - -
55A THR* 1.3 80.5 - - - +
57A VAL* 1.3 62.4 + - - +
58A PRO* 4.0 4.0 - - - +
96A SER 5.2 1.1 - - - +
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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