Contacts of the helix formed by residues 1 - 28 (chain A) in PDB entry 2LQ2
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 1 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 1.3 64.3 + - + +
3A GLY* 3.6 12.8 - - - +
4A ARG* 3.3 54.1 + - - +
5A ILE* 4.0 7.3 + - - +
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Residues in contact with LYS 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 1.3 73.4 - - + +
3A GLY* 1.3 60.6 + - - +
4A ARG 3.3 0.2 - - - -
5A ILE* 3.1 13.5 - - + +
6A ASP* 2.7 57.7 + - + +
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Residues in contact with GLY 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 3.2 10.3 - - - +
2A LYS* 1.3 87.3 - - - +
4A ARG* 1.3 69.1 + - - +
6A ASP* 3.6 9.0 - - - +
7A ALA* 3.3 22.0 + - - +
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Residues in contact with ARG 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 3.3 40.6 + - - +
2A LYS 3.3 0.4 - - - -
3A GLY* 1.3 83.2 - - - +
5A ILE* 1.3 56.5 + - + +
7A ALA* 4.0 2.5 - - - +
8A PRO* 2.8 22.5 - - - +
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Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL 4.0 4.4 + - - +
2A LYS* 3.1 28.5 - - + +
4A ARG* 1.3 77.7 - - - +
6A ASP* 1.3 60.7 + - - +
7A ALA 3.3 0.7 - - - -
8A PRO* 3.1 7.4 - - + +
9A ASP* 2.7 61.1 + - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 2.7 45.4 + - + +
3A GLY* 3.6 11.6 - - - +
4A ARG 3.3 0.2 - - - -
5A ILE* 1.3 73.1 - - - +
7A ALA* 1.3 57.9 + - - +
9A ASP* 3.6 5.2 - - - +
10A PHE* 2.7 60.6 + - - +
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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
----------------------------------------------------------
3A GLY 3.3 11.9 + - - +
4A ARG* 4.0 2.9 - - - +
6A ASP* 1.3 81.5 + - - +
8A PRO* 1.3 65.2 - - + +
10A PHE* 3.2 10.8 - - - +
11A PRO* 2.8 23.7 - - - +
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Residues in contact with PRO 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG 2.8 28.5 - - - +
5A ILE* 3.1 21.3 - - + +
7A ALA* 1.3 90.5 - - + +
9A ASP* 1.3 60.7 + - - +
11A PRO* 3.1 22.2 - - + +
12A SER* 3.7 10.6 + - - -
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Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 2.7 50.5 + - - +
6A ASP* 4.0 5.4 - - - +
8A PRO* 1.3 82.4 - - - +
10A PHE* 1.3 57.4 + - - +
11A PRO 3.4 0.2 - - - -
12A SER* 3.5 8.6 - - - -
13A SER* 2.7 36.4 + - - -
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 2.7 40.5 + - - +
7A ALA* 3.2 11.0 - - - +
9A ASP* 1.3 78.5 - - - +
11A PRO* 1.3 65.3 - - + +
13A SER* 3.2 7.8 - - - -
14A PRO* 2.8 23.9 - - - +
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Residues in contact with PRO 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 2.8 18.6 - - - +
8A PRO* 3.1 19.5 - - + +
10A PHE* 1.3 93.9 - - + +
12A SER* 1.3 56.1 + - - +
13A SER 3.2 0.2 - - - -
14A PRO* 3.0 22.1 - - + +
15A ALA* 3.8 8.0 + - - +
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Residues in contact with SER 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO 3.8 14.6 + - - -
9A ASP* 3.3 9.8 + - - -
10A PHE 3.2 0.4 - - - -
11A PRO* 1.3 79.2 - - - +
13A SER* 1.3 56.3 + - - +
14A PRO 3.4 0.2 - - - -
15A ALA* 3.6 8.9 - - - +
16A ILE* 2.7 49.3 + - - +
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 2.7 13.7 + - - -
10A PHE* 3.2 13.2 - - - -
12A SER* 1.3 76.8 - - - +
14A PRO* 1.3 64.2 - - - +
16A ILE* 4.0 3.3 - - - +
17A LEU* 3.0 44.7 + - - +
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Residues in contact with PRO 14 (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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10A PHE 2.8 19.1 - - - +
11A PRO* 3.0 20.6 - - + +
13A SER* 1.3 92.9 - - - +
15A ALA* 1.3 54.9 + - - +
17A LEU* 4.5 4.9 - - + +
18A GLY* 3.1 22.7 + - - -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO 4.0 10.8 - - - +
12A SER* 3.2 12.3 + - - +
14A PRO* 1.3 80.7 - - - +
16A ILE* 1.3 62.3 + - + +
19A LYS* 2.9 51.0 + - + +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 2.7 33.6 + - - +
13A SER* 4.1 3.6 - - - +
15A ALA* 1.3 73.3 - - + +
17A LEU* 1.3 64.4 + - + +
19A LYS* 4.1 5.1 - - + +
20A ALA* 3.0 32.0 + - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.0 31.0 + - - +
14A PRO* 4.5 4.0 - - + +
16A ILE* 1.3 81.1 - - + +
18A GLY* 1.3 60.3 + - - +
20A ALA* 4.2 5.4 - - + +
21A ALA* 3.6 20.4 + - - +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.1 19.4 + - - -
15A ALA 4.0 0.4 - - - -
17A LEU* 1.3 78.7 - - - +
19A LYS* 1.3 67.2 + - - +
21A ALA* 3.7 5.5 + - - +
22A THR* 3.4 21.0 + - - +
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Residues in contact with LYS 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 ALA* 2.9 40.2 + - + +
16A ILE* 4.1 6.7 - - + +
18A GLY* 1.3 79.1 - - - +
20A ALA* 1.3 56.9 + - - +
21A ALA 3.2 0.7 - - - -
22A THR* 3.1 10.6 - - + +
23A ASP* 2.8 50.3 + - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.0 22.8 + - + +
17A LEU* 4.2 7.2 - - + +
19A LYS* 1.3 78.9 - - - +
21A ALA* 1.3 58.5 + - - +
23A ASP* 4.1 5.6 - - - -
24A VAL* 2.9 35.8 + - + +
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Residues in contact with ALA 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 LEU 3.6 15.2 + - - +
18A GLY* 4.0 6.5 - - - +
19A LYS 3.2 0.4 - - - -
20A ALA* 1.3 80.2 - - - +
22A THR* 1.3 58.4 + - - +
24A VAL* 3.8 3.5 + - - +
25A VAL* 2.9 30.8 + - - +
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Residues in contact with THR 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 GLY 3.4 14.3 + - - +
19A LYS* 3.1 26.9 - - + +
21A ALA* 1.3 76.7 - - - +
23A ASP* 1.3 70.3 + - - +
25A VAL* 3.9 6.8 - - - +
26A ALA* 3.2 25.3 + - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 2.8 35.0 + - - +
20A ALA* 3.9 7.2 - - - +
21A ALA 3.3 0.2 - - - -
22A THR* 1.3 84.3 - - - +
24A VAL* 1.3 61.2 + - + +
26A ALA* 3.5 3.9 + - - +
27A ALA* 2.9 31.6 + - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 2.9 26.5 + - + +
21A ALA* 4.2 3.8 - - - +
23A ASP* 1.3 75.3 - - + +
25A VAL* 1.3 68.3 + - + +
27A ALA* 3.5 13.3 + - + +
28A TRP* 3.6 19.0 + - + +
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Residues in contact with VAL 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 ALA 2.9 25.1 + - - +
22A THR* 4.0 7.6 - - - +
23A ASP 3.3 0.4 - - - -
24A VAL* 1.3 81.0 - - + +
26A ALA* 1.3 58.8 + - - +
28A TRP* 3.4 18.8 - - - +
29A LYS 4.8 0.3 + - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.2 17.4 + - - +
23A ASP* 4.1 3.8 - - - +
25A VAL* 1.3 75.5 - - - +
27A ALA* 1.3 59.5 + - - +
28A TRP 2.9 6.2 + - - -
29A LYS* 2.9 43.6 + - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP 2.9 19.7 + - - +
24A VAL* 3.8 10.1 - - + +
25A VAL 3.4 0.4 - - - -
26A ALA* 1.3 77.6 - - - +
28A TRP* 1.3 63.1 + - - +
30A SER* 2.9 29.5 + - - +
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Residues in contact with TRP 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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24A VAL* 3.6 15.3 + - + +
25A VAL* 3.4 17.7 - - - +
26A ALA 2.9 0.6 - - - -
27A ALA* 1.3 79.6 - - - +
29A LYS* 1.3 59.6 + - - +
30A SER 4.4 3.5 - - - +
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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
------------------------------------------------------------
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