Contacts of the helix formed by residues 2 - 21 (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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY* 1.3 84.2 - - - +
3A GLU* 1.3 64.1 + - - +
4A LEU 3.5 1.8 + - - -
5A GLU* 3.1 23.2 + - - +
6A THR* 3.5 6.6 + - - -
14B VAL* 6.0 0.7 - - - -
18B HIS* 5.6 2.9 - - - -
39B THR* 5.0 3.3 + - - -
40B GLU* 3.1 51.0 + - - +
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Residues in contact with GLU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 1.3 74.9 - - - +
4A LEU* 1.3 58.0 + - - +
6A THR* 3.0 14.0 + - - -
7A ALA* 2.9 25.3 + - - +
10B THR* 3.5 25.5 - - + +
13B ASN* 4.3 11.1 + - - +
14B VAL* 3.5 22.4 - - + +
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.2 2.8 + - - +
3A GLU* 1.3 79.1 - - - +
5A GLU* 1.3 63.0 + - - +
7A ALA* 2.9 6.4 + - + +
8A MET* 2.9 30.7 + - + +
10B THR* 4.8 2.0 - - - -
11B LEU* 3.0 37.5 - - + -
14B VAL* 4.2 12.8 - - + +
37B LEU* 5.6 0.2 - - + -
40B GLU* 2.7 36.3 - - + +
41B LEU* 3.5 24.7 - - + -
74B TYR* 4.1 18.6 - - + +
78B VAL* 4.6 16.6 - - + -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 2.7 31.0 + - - -
2A SER* 3.1 14.2 + - - +
4A LEU* 1.3 78.5 - - - +
6A THR* 1.3 63.7 + - - +
8A MET* 3.5 20.2 + - + +
9A GLU* 3.4 35.4 + - - +
40B GLU 4.0 17.8 + - - +
41B LEU* 5.4 0.7 - - - -
44B PHE* 4.6 16.6 - - + -
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Residues in contact with THR 6 (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 GLY 5.2 1.4 + - - -
2A SER 3.5 9.2 + - - -
3A GLU* 3.0 12.8 + - - -
5A GLU* 1.3 80.0 - - - +
7A ALA* 1.3 49.7 + - - +
9A GLU* 3.2 15.8 + - - +
10A THR* 2.6 43.1 + - - +
13A ASN* 5.0 0.2 + - - -
10B THR* 6.1 0.2 - - - -
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Residues in contact with ALA 7 (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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3A GLU 2.9 12.1 + - - +
4A LEU* 2.9 14.3 + - + +
6A THR* 1.3 74.4 - - - +
8A MET* 1.3 66.9 + - - +
10A THR* 2.8 20.2 + - - -
11A LEU* 2.9 20.7 + - + +
7B ALA* 4.6 9.9 - - + -
10B THR* 4.2 18.2 - - + -
11B LEU* 4.2 17.5 - - + -
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Residues in contact with MET 8 (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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4A LEU* 2.9 25.0 + - + +
5A GLU* 3.9 20.0 - - + +
6A THR 3.4 0.2 - - - -
7A ALA* 1.3 76.1 - - - +
9A GLU* 1.3 65.9 + - + +
11A LEU* 3.4 17.1 + - + +
12A ILE* 3.4 20.8 + - - +
41B LEU* 3.5 40.2 - - + -
44B PHE* 4.4 20.4 - - + -
78B VAL* 5.5 7.4 - - + +
82B THR* 3.5 40.5 + - - +
85B CYS* 4.5 14.1 - - + -
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.4 29.9 - - + +
6A THR* 3.2 15.0 + - + +
7A ALA 3.1 0.2 - - - -
8A MET* 1.3 79.6 - - + +
10A THR* 1.3 52.2 + - - +
12A ILE* 3.3 8.5 + - + +
13A ASN* 2.4 55.6 + - - +
44B PHE* 5.6 6.2 - - + -
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Residues in contact with THR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 2.6 34.6 + - - +
7A ALA* 2.8 14.0 + - - -
9A GLU* 1.3 77.0 - - - +
11A LEU* 1.3 56.3 + - - -
13A ASN* 3.6 8.8 + - - +
14A VAL* 2.9 37.0 + - + +
3B GLU* 3.5 48.0 - - + +
4B LEU* 4.4 0.9 - - - +
7B ALA* 4.2 10.0 - - + +
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Residues in contact with LEU 11 (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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7A ALA* 2.9 15.9 + - + +
8A MET* 3.6 14.6 - - + +
9A GLU 3.3 0.2 - - - -
10A THR* 1.3 76.6 - - - +
12A ILE* 1.3 60.3 + - + +
14A VAL* 2.9 24.1 - - + +
15A PHE* 2.9 14.3 + - - +
71A PHE* 4.6 13.8 - - + -
75A VAL* 6.1 3.1 - - + -
78A VAL* 5.4 14.1 - - + -
4B LEU* 3.0 35.0 - - + -
7B ALA* 4.2 11.7 - - + -
11B LEU* 5.7 11.0 - - + -
79B ALA* 6.1 1.3 - - - -
82B THR* 4.7 17.3 - - + +
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Residues in contact with ILE 12 (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 MET 3.4 15.9 + - - +
9A GLU* 3.3 9.3 + - + +
10A THR 3.3 0.2 - - - -
11A LEU* 1.3 75.2 - - + +
13A ASN* 1.3 61.5 + - - +
15A PHE* 3.5 11.1 - - + +
16A HIS* 2.7 39.3 + - + +
71A PHE* 4.9 12.8 - - + -
82B THR* 4.3 12.6 - - - +
83B VAL* 6.1 0.2 - - - -
85B CYS* 4.4 6.3 - - - -
86B ASN* 2.9 42.0 - - - +
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Residues in contact with ASN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 5.0 0.2 + - - -
9A GLU* 2.4 52.0 + - - +
10A THR* 3.2 8.7 + - - +
12A ILE* 1.3 78.9 - - - +
14A VAL* 1.3 60.5 + - - +
16A HIS* 3.9 5.4 - - - +
17A ALA* 3.5 19.4 + - - +
3B GLU* 4.3 10.1 + - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR 2.9 20.0 + - - +
11A LEU* 2.9 29.6 - - - +
13A ASN* 1.3 73.5 - - - +
15A PHE* 1.3 66.0 + - - +
17A ALA* 3.3 3.6 + - - +
18A HIS* 2.8 36.8 + - + +
36A LEU* 5.9 0.7 - - + -
40A GLU* 3.8 24.9 - - - +
2B SER* 6.0 0.2 - - - -
3B GLU* 3.5 38.6 - - + +
4B LEU* 4.2 15.5 - - + +
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 2.9 19.0 + - - +
12A ILE* 3.5 11.0 - - + +
14A VAL* 1.3 80.7 - - + +
16A HIS* 1.3 61.9 + - + +
18A HIS* 4.9 2.2 - - - -
19A SER* 2.8 53.0 + - - +
25A LYS* 2.6 34.3 - - + -
26A TYR* 3.9 16.4 - + - -
27A LYS 4.4 2.7 - - - -
28A LEU* 3.6 25.4 - - + -
36A LEU* 5.0 6.3 - - + -
71A PHE* 3.0 57.0 - + + -
74A TYR* 5.5 0.7 - + - -
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Residues in contact with HIS 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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12A ILE* 2.7 23.8 + - + +
13A ASN* 3.9 7.2 - - - +
15A PHE* 1.3 80.2 - - + +
17A ALA* 1.3 65.9 + - - +
19A SER* 5.1 0.2 - - - -
20A GLY 3.4 13.2 + - - -
25A LYS* 3.2 57.5 + - + +
26A TYR* 5.1 7.8 + + - -
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Residues in contact with ALA 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 ASN 3.5 11.2 + - - +
14A VAL* 3.3 8.4 + - - +
15A PHE 3.3 0.4 - - - -
16A HIS* 1.3 86.3 + - - +
18A HIS* 1.3 71.4 + - + +
20A GLY* 3.5 6.8 + - - -
21A LYS* 3.8 12.4 + - - +
25A LYS* 5.5 0.4 + - - +
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Residues in contact with HIS 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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14A VAL* 2.8 34.1 + - - +
15A PHE 4.3 0.7 - - - +
17A ALA* 1.3 79.6 - - + +
19A SER* 1.3 65.7 + - - +
21A LYS* 3.0 51.6 + - - +
32A GLU* 3.9 6.5 - - + +
36A LEU* 3.0 39.8 - - + +
39A THR* 5.1 11.2 - - + +
40A GLU* 3.1 20.2 + - - +
2B SER* 5.6 2.6 - - - -
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Residues in contact with SER 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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15A PHE* 2.8 49.0 + - - -
18A HIS* 1.3 74.5 - - - +
20A GLY* 1.3 57.2 + - - +
22A GLU 2.7 7.3 - - - +
23A GLY 4.3 0.3 - - - +
24A ASP 4.0 0.9 - - - +
25A LYS* 2.9 29.1 - - - -
27A LYS 4.3 0.2 - - - -
28A LEU* 4.2 3.5 - - - +
32A GLU* 2.6 23.0 + - - +
36A LEU* 5.0 1.0 - - - +
201A CA 2.5 24.8 - - - -
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Residues in contact with GLY 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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16A HIS 3.4 8.9 + - - -
17A ALA 3.5 3.8 + - - -
18A HIS 3.1 1.4 - - - -
19A SER* 1.3 76.7 - - - +
21A LYS* 1.3 64.3 + - - +
22A GLU* 3.2 3.5 + - - -
23A GLY 4.5 4.9 - - - +
25A LYS* 3.7 35.3 - - - +
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Residues in contact with LYS 21 (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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17A ALA 3.8 10.4 + - - +
18A HIS* 3.0 44.0 + - - +
20A GLY* 1.3 78.4 - - - +
22A GLU* 1.3 71.4 + - + +
31A LYS* 6.5 1.1 - - - +
32A GLU* 4.5 8.1 - - - +
35A GLU* 4.6 19.1 - - - +
36A LEU* 5.4 1.2 - - - +
39A THR* 6.1 2.0 - - - +
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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