Contacts of the helix formed by residues 51 - 62 (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 VAL 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.6 10.8 - - - +
47A ALA* 3.8 5.4 - - - +
48A GLN* 4.2 17.0 + - - +
49A LYS 4.1 0.4 - - - -
50A ASP* 1.3 73.1 - - - +
52A ASP* 1.3 65.0 + - - +
54A VAL* 3.0 28.4 + - + +
55A ASP* 4.3 1.6 + - - +
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Residues in contact with ASP 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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50A ASP* 3.2 3.1 - - + -
51A VAL* 1.3 80.5 - - - +
53A ALA* 1.3 62.5 + - - +
54A VAL 3.1 1.0 + - - -
55A ASP* 3.1 29.4 + - - +
56A LYS* 3.6 17.8 + - - +
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Residues in contact with ALA 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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47A ALA* 5.9 3.4 - - + -
50A ASP* 3.1 30.6 + - + +
51A VAL 3.1 0.4 - - - -
52A ASP* 1.3 79.8 - - - +
54A VAL* 1.3 62.1 + - + +
56A LYS* 3.0 15.2 + - + +
57A VAL* 2.9 29.1 + - + +
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Residues in contact with VAL 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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30A LYS* 4.9 15.5 - - + +
33A LEU* 5.5 6.6 - - + +
34A LYS* 3.6 49.4 - - + +
47A ALA* 4.1 15.7 - - + -
50A ASP 4.8 0.2 - - - +
51A VAL* 3.0 19.1 + - + +
53A ALA* 1.3 77.7 - - - +
55A ASP* 1.3 71.1 + - - +
57A VAL* 3.1 9.7 + - + +
58A MET* 2.9 22.8 + - + +
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Residues in contact with ASP 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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30A LYS* 3.7 25.1 + - - -
51A VAL 5.3 0.9 - - - -
52A ASP* 3.1 23.2 + - - +
54A VAL* 1.3 80.5 - - - +
56A LYS* 1.3 67.1 + - + +
58A MET* 3.2 11.7 - - + +
59A LYS* 2.9 24.8 + - - +
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Residues in contact with LYS 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 ASP* 3.8 24.9 - - - +
53A ALA* 3.0 14.5 + - + +
55A ASP* 1.3 79.8 - - + +
57A VAL* 1.3 63.7 + - + +
59A LYS* 3.4 13.0 + - + +
60A GLU* 3.4 20.7 + - - +
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Residues in contact with VAL 57 (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* 4.9 2.9 - - + -
37A LEU* 4.4 19.7 - - + -
53A ALA* 2.9 22.8 + - + +
54A VAL* 3.1 10.3 + - + +
56A LYS* 1.3 76.1 - - + +
58A MET* 1.3 65.7 + - - +
60A GLU* 3.2 20.1 + - - +
61A LEU* 3.2 20.0 + - + +
77A LEU* 3.7 24.9 - - + +
81A LEU* 5.7 1.6 - - + -
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Residues in contact with MET 58 (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* 3.5 37.9 - - + -
33A LEU* 4.5 9.4 - - + +
54A VAL* 2.9 14.0 + - + +
55A ASP* 3.2 19.7 - - + +
57A VAL* 1.3 73.6 - - - +
59A LYS* 1.3 79.9 + - + +
61A LEU* 2.9 15.1 + - - +
62A ASP* 2.9 29.8 + - - +
67A GLY* 2.7 38.1 - - - +
69A VAL* 4.1 15.4 - - + +
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Residues in contact with LYS 59 (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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55A ASP 2.9 13.4 + - - +
56A LYS* 3.5 10.5 - - + +
57A VAL 3.2 0.2 - - - -
58A MET* 1.3 93.0 - - + +
60A GLU* 1.3 62.8 + - + +
62A ASP* 3.4 19.4 + - + +
65A GLY* 6.3 1.0 - - - -
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Residues in contact with GLU 60 (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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56A LYS* 3.6 15.0 - - - +
57A VAL* 3.2 12.4 + - - +
58A MET 3.2 0.4 - - - -
59A LYS* 1.3 78.5 - - + +
61A LEU* 1.3 65.4 + - + +
62A ASP 3.5 3.1 + - - -
63A GLU* 4.4 7.6 + - - +
77A LEU* 4.2 19.3 - - + +
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Residues in contact with LEU 61 (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* 3.6 37.5 - - + -
37A LEU* 5.9 0.2 - - + -
57A VAL* 3.3 16.2 - - + +
58A MET* 2.9 7.5 + - - +
60A GLU* 1.3 80.0 - - - +
62A ASP* 1.3 51.6 + - - +
63A GLU* 2.9 5.9 + - - +
69A VAL* 3.5 25.1 - - + -
73A GLU* 2.4 51.4 - - + +
74A TYR* 4.3 6.3 - - + -
77A LEU* 3.3 47.1 - - + -
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Residues in contact with ASP 62 (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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58A MET* 2.9 25.0 + - - +
59A LYS* 3.4 14.4 + - + +
60A GLU 3.3 1.9 - - - -
61A LEU* 1.3 73.8 - - - +
63A GLU* 1.3 59.8 + - - +
64A ASN 3.4 0.3 + - - -
65A GLY* 2.6 20.9 + - - -
66A ASP* 2.3 23.8 + - - +
67A GLY* 2.4 26.1 + - - +
68A GLU 4.1 4.3 - - - +
69A VAL* 4.6 0.4 - - + +
73A GLU* 3.3 5.8 + - - -
202A CA 2.2 29.6 - - - -
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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