Contacts of the helix formed by residues 6 - 31 (chain A) in PDB entry 2LJT
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 GLY 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR 5.3 0.6 + - - -
4A GLY* 3.3 4.5 - - - -
5A ASN* 1.3 79.9 - - - +
7A VAL* 1.3 63.1 + - - +
8A HIS* 3.3 3.4 - - - +
9A LEU* 3.3 22.2 + - - +
10A THR* 2.8 25.8 + - - -
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 4.8 14.1 - - + +
6A GLY* 1.3 82.3 - - - +
8A HIS* 1.3 67.7 + - + +
10A THR* 3.3 14.9 + - - -
11A LYS* 3.4 25.6 - - + +
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Residues in contact with HIS 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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3A TYR 5.5 5.8 - - - +
4A GLY* 6.0 3.6 - - - -
5A ASN 6.2 0.4 - - - +
6A GLY* 3.3 2.1 - - - +
7A VAL* 1.3 83.1 - - + +
9A LEU* 1.3 59.6 + - - +
11A LYS* 4.0 5.4 - - + +
12A SER* 2.9 42.4 + - - -
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Residues in contact with LEU 9 (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 TYR* 5.2 13.8 + - + +
6A GLY* 3.3 22.7 + - - +
7A VAL 3.2 0.4 - - - -
8A HIS* 1.3 77.8 - - - +
10A THR* 1.3 68.6 + - - +
12A SER* 4.0 5.4 - - - -
13A GLY 3.1 18.4 + - - -
14A LEU* 3.3 6.0 + - - -
17A ASN* 3.1 48.0 - - + +
18A TRP* 3.7 18.4 - - + -
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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 GLY 2.8 17.2 + - - -
7A VAL* 3.3 11.3 + - - -
8A HIS 3.2 0.4 - - - -
9A LEU* 1.3 78.7 - - + +
11A LYS* 1.3 75.0 + - + +
12A SER 4.0 0.2 - - - -
13A GLY* 4.1 0.2 - - - -
14A LEU* 3.0 57.8 + - + +
18A TRP* 5.8 3.8 - - + -
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Residues in contact with LYS 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 VAL* 3.4 21.4 + - - +
8A HIS* 4.4 5.6 - - + +
10A THR* 1.3 85.6 - - + +
12A SER* 1.3 63.9 + - - +
14A LEU* 5.8 0.2 - - - -
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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 HIS* 2.9 36.5 + - - -
9A LEU* 3.7 7.0 - - - -
11A LYS* 1.3 81.8 - - - +
13A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.1 6.1 + - - -
10A THR 4.1 0.2 - - - -
12A SER* 1.3 83.6 + - - +
14A LEU* 1.3 57.1 + - - +
15A SER* 3.0 4.5 - - - -
16A VAL* 2.9 20.9 - - - +
17A ASN* 2.7 35.7 + - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.3 5.8 + - - -
10A THR* 3.0 48.4 + - + +
11A LYS* 5.8 0.2 - - - -
13A GLY* 1.3 74.1 - - - +
15A SER* 1.3 72.3 + - - +
17A ASN* 4.1 5.2 - - - -
18A TRP* 3.1 52.0 + - + +
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Residues in contact with SER 15 (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 GLY* 3.0 1.9 - - - -
14A LEU* 1.3 90.0 - - - +
16A VAL* 1.3 60.7 + - - +
18A TRP* 4.1 2.2 - - - +
19A GLY* 3.1 25.1 + - - -
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Residues in contact with VAL 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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13A GLY* 2.9 34.0 - - - +
15A SER* 1.3 79.5 - - - +
17A ASN* 1.3 62.3 + - + +
19A GLY* 4.1 1.3 - - - +
20A GLU* 3.2 45.7 + - + +
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.1 37.5 - - + +
13A GLY 2.7 17.4 + - - +
14A LEU 3.8 4.5 - - - +
16A VAL* 1.3 77.8 - - + +
18A TRP* 1.3 94.1 + - + +
20A GLU* 3.3 10.9 + - - +
21A ALA* 3.1 23.2 + - - +
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Residues in contact with TRP 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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9A LEU* 3.7 18.8 - - + -
10A THR* 5.8 4.3 - - + -
14A LEU* 3.1 42.9 + - + +
15A SER* 4.1 3.1 - - - +
17A ASN* 1.3 108.2 - - - +
19A GLY* 1.3 63.9 + - - +
21A ALA* 3.2 7.9 + - + +
22A PHE* 3.0 23.5 + - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 3.1 16.3 + - - -
16A VAL* 4.3 1.6 - - - -
18A TRP* 1.3 77.2 - - - +
20A GLU* 1.3 61.6 + - - +
22A PHE* 3.5 7.3 + - - +
23A SER* 3.1 25.6 + - - -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.2 42.3 + - + +
17A ASN* 3.6 10.8 + - - +
18A TRP 3.2 0.8 - - - -
19A GLY* 1.3 75.4 - - - +
21A ALA* 1.3 63.3 + - - +
22A PHE 3.4 0.3 + - - -
23A SER* 3.5 14.7 + - - -
24A ALA* 3.5 13.3 + - - +
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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
----------------------------------------------------------
17A ASN* 3.1 15.7 + - - +
18A TRP* 3.2 10.5 + - - +
20A GLU* 1.3 78.3 - - - +
22A PHE* 1.3 61.6 + - - +
24A ALA* 3.7 5.4 + - - +
25A GLY* 3.2 17.7 + - - -
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Residues in contact with PHE 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 TRP 3.0 15.5 + - - +
19A GLY* 3.7 9.2 - - - +
20A GLU 3.2 0.2 - - - -
21A ALA* 1.3 76.4 - - - +
23A SER* 1.3 66.4 + - - +
25A GLY* 3.0 4.1 + - - -
26A VAL* 2.9 44.1 + - + +
29A LEU* 5.6 10.5 - - + -
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Residues in contact with SER 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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19A GLY 3.1 13.2 + - - -
20A GLU* 3.6 10.8 - - - -
22A PHE* 1.3 79.0 - - - +
24A ALA* 1.3 63.5 + - - +
26A VAL* 3.0 25.9 + - - +
27A HIS* 3.7 3.8 + - - +
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Residues in contact with ALA 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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20A GLU 3.5 9.1 + - - +
21A ALA* 4.0 7.6 - - - +
22A PHE 3.3 0.4 - - - -
23A SER* 1.3 79.4 - - - +
25A GLY* 1.3 62.6 + - - +
27A HIS* 3.3 20.8 + - - +
28A ARG* 3.8 4.3 + - - +
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Residues in contact with GLY 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 3.2 11.8 + - - -
22A PHE* 3.0 9.1 + - - -
24A ALA* 1.3 75.6 - - - +
26A VAL* 1.3 64.3 + - - +
28A ARG* 3.0 19.3 + - - +
29A LEU* 3.1 19.5 + - - +
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Residues in contact with VAL 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 PHE* 2.9 47.9 + - + +
23A SER* 3.0 12.5 + - - +
25A GLY* 1.3 77.0 - - - +
27A HIS* 1.3 57.1 - - - +
29A LEU* 3.3 12.5 + - + +
30A ALA* 3.0 31.1 + - + +
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Residues in contact with HIS 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 SER 3.7 3.2 + - - +
24A ALA* 3.3 15.4 + - - +
25A GLY 3.1 0.8 - - - -
26A VAL* 1.3 80.2 - - - +
28A ARG* 1.3 60.5 + - - +
30A ALA* 3.6 3.3 + - - -
31A ASN* 3.1 45.6 + - - +
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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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24A ALA 3.8 4.2 + - - +
25A GLY* 3.0 13.7 + - - +
27A HIS* 1.3 77.6 - - - +
29A LEU* 1.3 70.5 + - + +
31A ASN* 3.4 25.7 + - - +
32A GLY* 3.7 5.7 + - - -
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Residues in contact with LEU 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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22A PHE* 5.6 8.7 - - + -
25A GLY 3.1 16.8 + - - +
26A VAL* 3.6 17.7 - - + +
28A ARG* 1.3 81.1 - - + +
30A ALA* 1.3 66.4 + - - +
32A GLY* 3.6 6.2 + - - -
33A GLY* 3.7 9.5 + - - -
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Residues in contact with ALA 30 (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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26A VAL* 3.0 20.3 + - + +
27A HIS* 3.9 5.2 - - - +
29A LEU* 1.3 77.6 - - - +
31A ASN* 1.3 65.2 + - - +
32A GLY 3.1 6.1 + - - -
33A GLY 4.2 1.9 + - - -
34A ASN 4.2 11.1 + - - +
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Residues in contact with ASN 31 (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 HIS* 3.1 48.6 + - - +
28A ARG* 3.4 16.5 + - - +
30A ALA* 1.3 80.0 - - - +
32A GLY* 1.3 55.2 + - - +
34A ASN 5.2 2.0 - - - -
37A TRP* 4.8 18.9 + - + -
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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