Contacts of the helix formed by residues 12 - 29 (chain A) in PDB entry 2LPN
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 GLU 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A CYS* 1.3 84.4 - - - +
13A VAL* 1.3 58.0 + - - +
14A CYS 3.1 0.6 - - - +
15A LYS* 2.8 16.0 + - + +
16A GLU* 2.7 42.7 + - + +
101A LYS* 3.4 31.1 + - + +
102A TYR* 3.0 47.4 + - + +
103A GLU 4.6 0.9 + - - -
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Residues in contact with VAL 13 (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 GLU* 1.3 78.6 - - - +
14A CYS* 1.3 63.0 + - - +
17A PHE* 3.0 20.1 + - - +
51A LYS* 3.7 26.7 - - + +
52A GLU* 4.2 3.1 - - + -
55A LEU* 3.2 27.5 - - + +
99A GLU 3.6 10.3 + - - +
100A LEU* 3.0 37.5 - - + +
101A LYS* 3.9 4.0 - - - -
102A TYR* 3.6 40.5 + - + +
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Residues in contact with CYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS* 4.7 5.8 - - + -
12A GLU 3.1 1.0 - - - +
13A VAL* 1.3 79.2 - - - +
15A LYS* 1.3 59.4 + - - +
17A PHE* 4.0 1.0 - - - +
18A LEU* 3.1 38.3 + - - +
55A LEU* 3.5 13.3 - - + +
59A LEU* 4.9 3.1 - - - +
87A CYS* 2.0 51.6 - - - -
90A LEU* 3.9 6.7 - - - -
97A ILE* 3.8 37.5 + - + +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.5 27.6 + - + +
7A PRO* 5.7 0.4 - - - +
8A GLY* 3.1 13.8 - - - +
9A ALA* 3.0 34.3 + - + +
10A ASP* 3.2 31.1 + - - +
11A CYS 3.2 13.0 + - - -
12A GLU* 2.8 29.6 + - + +
14A CYS* 1.3 74.1 - - - +
16A GLU* 1.3 74.3 + - - +
18A LEU 3.4 0.3 + - - -
19A ASN* 2.9 27.0 + - - +
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Residues in contact with GLU 16 (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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6A ARG* 2.6 59.3 + - - +
8A GLY* 4.7 1.6 + - - -
12A GLU* 2.7 28.9 + - + +
15A LYS* 1.3 85.4 - - - +
17A PHE* 1.3 62.3 + - - +
19A ASN* 4.8 2.7 - - - +
20A ARG* 3.0 47.7 + - - +
102A TYR* 3.3 33.7 - - + +
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Residues in contact with PHE 17 (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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13A VAL 3.0 18.7 + - - +
14A CYS 4.0 0.9 - - - +
16A GLU* 1.3 77.2 - - - +
18A LEU* 1.3 67.5 + - + +
20A ARG* 4.0 1.8 - - - +
21A PHE* 2.8 45.5 + + + +
41A LEU* 3.6 24.2 - - + -
44A PHE* 3.5 33.1 - + + -
45A CYS* 3.4 27.8 - - - -
52A GLU* 4.2 22.9 - - + +
55A LEU* 3.7 11.7 - - + -
56A CYS* 3.4 16.2 - - - -
59A LEU* 3.7 29.2 - - + -
73A VAL* 5.7 1.3 - - + -
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Residues in contact with LEU 18 (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 GLY 4.5 2.9 - - - +
9A ALA* 3.9 2.0 - - + -
14A CYS* 3.1 25.1 + - - +
15A LYS 3.9 2.5 - - - +
17A PHE* 1.3 91.3 - - + +
19A ASN* 1.3 54.9 + - - +
21A PHE* 3.7 1.8 - - - +
22A TYR* 2.8 39.3 + - - +
59A LEU* 4.6 8.3 - - + -
73A VAL* 4.5 15.0 - - + -
77A MET* 3.5 26.3 - - + +
83A ALA* 3.6 26.2 - - + +
86A ILE* 4.9 5.8 - - + -
87A CYS* 3.6 27.1 - - + +
90A LEU* 4.3 8.5 - - + -
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Residues in contact with ASN 19 (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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2A GLU* 3.8 13.2 - - - +
3A ALA* 3.7 23.5 + - - +
6A ARG* 5.7 1.6 - - - -
7A PRO* 3.3 28.7 + - - +
8A GLY* 3.2 26.3 + - - -
15A LYS 2.9 9.6 + - - +
16A GLU* 4.2 4.0 - - - +
18A LEU* 1.3 76.7 - - - +
20A ARG* 1.3 59.8 + - + +
22A TYR* 3.2 10.6 + - - +
23A LYS* 3.0 36.5 + - - +
83A ALA* 6.4 0.7 - - - -
84A MET* 5.6 1.6 - - - +
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Residues in contact with ARG 20 (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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1A GLN* 4.5 14.8 - - + +
2A GLU* 3.4 41.2 - - + +
6A ARG* 3.3 30.4 - - - +
16A GLU* 3.0 34.2 + - - +
17A PHE 4.2 0.4 - - - +
19A ASN* 1.3 76.7 - - + +
21A PHE* 1.3 59.1 + - - +
23A LYS* 3.8 9.3 - - - +
24A SER* 2.9 30.3 + - - -
44A PHE* 4.4 14.8 - - + -
52A GLU* 2.6 35.8 + - - -
102A TYR* 2.8 25.5 + - - -
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Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.8 33.9 + + + +
18A LEU* 3.7 2.7 - - - +
20A ARG* 1.3 76.6 - - - +
22A TYR* 1.3 63.2 + - - +
24A SER* 3.5 4.3 - - - -
25A LEU* 3.1 62.3 + - + +
28A ARG* 6.0 0.2 - - - -
37A ILE* 3.6 12.6 - - + -
40A GLU 3.3 24.0 - - - -
41A LEU* 3.4 44.6 - - + -
44A PHE* 3.6 31.7 - + + -
73A VAL* 5.3 0.4 - - + -
77A MET* 4.3 19.1 - - + -
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Residues in contact with TYR 22 (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 LEU 2.8 20.9 + - - +
19A ASN* 3.4 10.8 - - - +
21A PHE* 1.3 83.8 - - - +
23A LYS* 1.3 64.5 + - + +
25A LEU* 3.4 3.5 + - - +
26A ILE* 3.1 39.2 + - + +
31A ASN* 5.7 0.4 - - - -
76A PRO 3.9 2.9 - - - -
77A MET* 3.6 55.9 - - + -
79A VAL 2.7 21.8 + - - -
80A HIS* 2.8 21.3 - + - -
81A MET 2.7 22.6 + - - -
83A ALA* 4.3 17.3 - - + -
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Residues in contact with LYS 23 (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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1A GLN* 3.9 18.5 + - - +
2A GLU 2.8 42.4 + - - +
3A ALA* 5.1 2.9 - - + +
19A ASN* 3.0 27.9 + - - +
20A ARG 3.8 5.6 - - - +
22A TYR* 1.3 78.9 - - + +
24A SER* 1.3 66.0 + - - +
26A ILE* 3.9 8.9 - - - +
27A ASP* 2.9 39.1 + - - +
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Residues in contact with SER 24 (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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1A GLN* 5.2 9.1 + - - +
20A ARG 2.9 22.5 + - - -
21A PHE* 3.5 7.4 - - - -
23A LYS* 1.3 82.8 - - - +
25A LEU* 1.3 56.3 + - - +
27A ASP* 3.1 3.9 + - - +
28A ARG* 2.6 71.0 + - - +
44A PHE* 4.5 9.7 - - - -
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Residues in contact with LEU 25 (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 PHE* 3.1 60.2 + - + +
22A TYR* 3.9 3.6 - - - +
24A SER* 1.3 79.6 - - - +
26A ILE* 1.3 62.8 + - - +
28A ARG* 4.1 12.1 - - - +
29A GLY* 3.0 2.8 + - - -
30A VAL* 2.8 62.6 + - + +
31A ASN* 3.7 27.8 + - - +
37A ILE* 3.8 14.8 - - + -
40A GLU* 4.1 11.2 - - + -
44A PHE* 5.8 0.4 - - + -
77A MET* 5.5 1.1 - - + -
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Residues in contact with ILE 26 (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 TYR* 3.1 32.9 + - + +
23A LYS* 3.9 7.9 - - - +
25A LEU* 1.3 77.0 - - - +
27A ASP* 1.3 61.2 + - - +
29A GLY* 3.4 10.7 + - - -
31A ASN* 3.9 28.9 - - + +
32A PHE* 5.0 15.0 - - + -
77A MET 4.3 6.7 - - - +
78A SER 5.5 2.2 - - - +
79A VAL* 5.7 3.1 - - - +
80A HIS* 5.9 1.1 - - - +
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Residues in contact with ASP 27 (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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23A LYS* 2.9 27.8 + - - +
24A SER* 3.7 3.8 - - - +
26A ILE* 1.3 76.3 - - - +
28A ARG* 1.3 66.6 + - + +
29A GLY* 3.0 6.4 + - - -
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Residues in contact with ARG 28 (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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1A GLN* 5.9 0.4 + - - -
24A SER* 2.6 44.9 + - - +
25A LEU* 4.1 11.1 - - - +
27A ASP* 1.3 76.3 - - - +
29A GLY* 1.3 60.2 + - - +
30A VAL* 3.3 19.5 + - + +
40A GLU* 2.8 30.1 + - - +
43A SER* 5.8 2.2 - - - -
44A PHE* 4.9 16.4 - - - +
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Residues in contact with GLY 29 (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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25A LEU 3.0 6.3 + - - -
26A ILE 3.8 7.4 - - - -
27A ASP 3.0 7.3 + - - -
28A ARG* 1.3 79.7 - - - +
30A VAL* 1.3 58.2 + - - +
31A ASN 3.4 6.6 + - - +
32A PHE* 6.4 0.9 - - - -
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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
------------------------------------------------------------
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