Contacts of the helix formed by residues 0 - 23 (chain A) in PDB entry 6LGV
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 HIS 0 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-4A ARG* 3.0 20.8 + - + +
-3A ALA* 3.2 7.8 + - - +
-1A HIS* 1.3 79.4 + - - +
1A MET* 1.3 69.8 + - - +
3A VAL* 3.3 10.5 + - + +
4A LYS* 2.9 36.3 + - + +
7A ARG* 5.2 10.8 - - - -
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Residues in contact with MET 1 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A ALA* 2.9 20.4 + - + +
-2A HIS* 3.7 13.2 - - - +
-1A HIS 3.2 0.2 - - - -
0A HIS* 1.3 82.5 - - + +
2A LEU* 1.3 58.6 + - + +
4A LYS* 3.2 9.5 + - + +
5A ILE* 2.9 52.1 + - + +
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Residues in contact with LEU 2 (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 HIS* 3.3 41.7 + - + +
-1A HIS 3.2 7.0 + - - +
1A MET* 1.3 75.0 - - + +
3A VAL* 1.3 60.3 + - - +
5A ILE* 4.0 7.7 - - + +
6A THR* 2.7 36.2 + - - -
110A VAL* 4.5 27.1 - - + -
113A TYR* 3.8 29.2 - - + -
114A LEU* 4.3 11.2 - - + -
187A PRO 5.7 2.5 - - - +
190A PRO* 4.9 13.0 - - + -
194A MET* 6.5 0.2 - - + -
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A HIS* 3.0 44.9 + - + +
0A HIS* 3.6 14.8 - - + +
2A LEU* 1.3 77.9 - - - +
4A LYS* 1.3 63.4 + - - +
6A THR* 3.4 1.2 + - - -
7A ARG* 3.0 61.4 + - + +
114A LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A HIS* 2.9 29.4 + - + +
1A MET* 3.6 15.0 - - + +
3A VAL* 1.3 79.8 - - - +
5A ILE* 1.3 67.9 + - + +
7A ARG* 3.7 12.9 - - + +
8A LEU* 3.1 51.2 + - + +
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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
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1A MET* 2.9 34.4 + - + +
2A LEU* 4.3 7.4 - - + +
4A LYS* 1.3 82.9 - - + +
6A THR* 1.3 57.5 + - - +
8A LEU* 3.3 20.2 + - + +
9A PHE* 2.9 28.3 + - + +
191A ALA* 4.4 20.4 - - + -
194A MET* 3.6 23.1 - - + -
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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
----------------------------------------------------------
2A LEU 2.7 23.2 + - - -
3A VAL 3.9 1.8 - - - -
5A ILE* 1.3 74.5 - - - +
7A ARG* 1.3 59.5 + - + +
9A PHE* 3.6 5.3 - - - +
10A CYS* 2.8 45.2 + - - -
110A VAL* 3.4 22.5 - - - +
111A MET* 3.8 30.3 - - + -
114A LEU* 3.5 15.3 - - + +
194A MET* 3.9 8.2 - - + +
294A ALA* 5.0 4.9 - - + -
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Residues in contact with ARG 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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0A HIS* 5.2 10.1 - - - -
3A VAL* 3.0 44.9 + - + +
4A LYS* 3.7 13.1 - - + +
6A THR* 1.3 76.6 - - - +
8A LEU* 1.3 63.4 + - + +
10A CYS* 3.4 5.4 + - - +
11A VAL* 3.1 31.5 + - + +
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Residues in contact with LEU 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 LYS* 3.1 50.9 + - + +
5A ILE* 3.7 20.0 - - + +
6A THR 3.3 0.2 - - - -
7A ARG* 1.3 75.7 - - + +
9A PHE* 1.3 67.1 + - - +
11A VAL* 4.0 2.2 - - - -
12A TRP* 3.0 50.1 + - + +
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Residues in contact with PHE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 2.9 18.1 + - + +
6A THR 3.6 2.5 - - - +
8A LEU* 1.3 75.1 - - - +
10A CYS* 1.3 69.6 + - - +
12A TRP 3.7 0.2 - - - -
13A ALA* 2.8 35.2 + - + +
111A MET* 4.0 21.8 - - + -
194A MET* 3.6 53.2 - - + -
197A ILE* 3.8 22.2 - - + -
198A LEU* 3.8 30.3 - - + +
201A ILE* 5.0 0.4 - - + -
287A ASN* 3.6 30.7 - - + -
291A CYS* 4.3 7.9 - - - -
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Residues in contact with CYS 10 (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 THR* 2.8 39.9 + - - +
7A ARG* 3.8 5.6 - - - +
8A LEU 3.2 0.2 - - - -
9A PHE* 1.3 84.0 - - - +
11A VAL* 1.3 63.7 + - + +
13A ALA* 3.5 4.4 + - - +
14A LEU* 3.3 20.4 + - - +
111A MET* 4.2 0.2 - - - -
288A LEU* 4.1 6.1 - - - +
291A CYS* 2.0 57.0 - - + -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.1 19.6 + - + +
8A LEU* 4.3 2.9 - - - +
10A CYS* 1.3 77.4 - - + +
12A TRP* 1.3 64.1 + - + +
14A LEU* 3.3 15.0 + - + +
15A LEU* 2.9 44.0 + - + +
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Residues in contact with TRP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.0 48.0 + - + +
9A PHE 4.1 2.0 - - - +
11A VAL* 1.3 77.0 - - + +
13A ALA* 1.3 59.7 + - - +
15A LEU* 3.7 33.9 - - + -
16A LEU* 2.8 52.4 + - + +
198A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 2.8 29.8 + - + +
10A CYS* 3.7 7.6 - - - +
11A VAL 3.3 0.2 - - - -
12A TRP* 1.3 77.0 - - - +
14A LEU* 1.3 60.9 + - - +
16A LEU* 4.2 1.6 - - - +
17A SER* 3.0 27.9 + - - -
198A LEU* 3.5 15.6 - - + +
201A ILE* 4.3 21.8 - - + +
284A VAL* 5.3 0.6 - - - +
287A ASN* 5.0 3.8 - - + -
288A LEU* 4.4 12.3 - - + -
291A CYS* 5.7 0.7 - - - -
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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
----------------------------------------------------------
10A CYS 3.3 8.9 + - - +
11A VAL* 3.3 17.8 + - + +
12A TRP 3.2 0.2 - - - -
13A ALA* 1.3 80.7 - - - +
15A LEU* 1.4 66.4 + - + +
17A SER* 3.1 7.8 + - - +
18A VAL* 3.1 40.8 + - + +
288A LEU* 4.0 26.8 - - + +
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Residues in contact with LEU 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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11A VAL* 2.9 37.7 + - + +
12A TRP* 3.4 43.0 + - + -
14A LEU* 1.4 78.8 - - + +
16A LEU* 1.3 58.1 + - - +
18A VAL* 3.3 5.8 + - + +
19A ALA* 2.8 28.9 + - - +
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Residues in contact with LEU 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 TRP* 2.8 44.9 + - + +
13A ALA* 4.3 2.5 - - - +
15A LEU* 1.3 69.9 - - - +
17A SER* 1.3 60.7 + - - +
19A ALA* 3.7 5.4 - - + +
20A ALA* 2.8 33.3 + - - +
27A PHE* 3.9 28.7 - - + -
198A LEU* 4.0 31.6 - - + +
201A ILE* 5.6 1.6 - - + -
202A SER* 3.6 20.0 - - - +
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Residues in contact with SER 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 ALA 3.0 17.3 + - - -
14A LEU* 3.1 15.2 + - - +
16A LEU* 1.3 76.0 - - - +
18A VAL* 1.3 68.7 + - - +
20A ALA* 4.5 1.1 - - - -
21A TYR* 3.1 19.8 + - - +
201A ILE* 4.1 10.2 - - - +
205A VAL* 3.6 16.9 - - - +
284A VAL* 3.6 40.6 - - - +
288A LEU* 5.1 0.2 - - - +
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Residues in contact with VAL 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 LEU* 3.1 31.1 + - + +
15A LEU* 3.8 5.2 - - + +
17A SER* 1.3 80.3 + - - +
19A ALA* 1.3 66.3 + - - +
21A TYR* 3.2 6.3 + - + +
22A PHE* 3.0 51.6 + - + -
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Residues in contact with ALA 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 LEU 2.8 21.5 + - - +
16A LEU* 3.3 7.8 + - + +
18A VAL* 1.3 71.4 - - - +
20A ALA* 1.4 53.4 + - - +
22A PHE* 3.3 4.3 + - - +
23A ARG* 2.8 40.2 + - + +
27A PHE* 3.7 18.9 - - + -
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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
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16A LEU 2.8 21.9 + - - +
19A ALA* 1.4 70.4 - - - +
21A TYR* 1.3 62.5 + - - +
23A ARG 4.5 0.2 - - - -
24A PRO* 3.2 25.8 - - - +
27A PHE* 3.5 22.0 - - + -
202A SER* 3.6 27.8 - - - +
205A VAL* 3.7 17.3 - - + -
206A ALA* 3.9 6.7 - - - +
209A GLN* 4.1 0.7 - - - +
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Residues in contact with TYR 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 SER 3.1 14.4 + - - +
18A VAL* 3.2 8.7 + - - +
20A ALA* 1.3 77.9 - - - +
22A PHE* 1.3 95.4 + + - +
24A PRO* 3.6 1.0 - - - +
205A VAL* 3.6 8.4 - - + +
209A GLN* 3.2 47.6 + - + +
212A ILE* 3.9 45.4 - - + +
213A ALA* 5.8 1.2 + - - -
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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 VAL* 3.0 49.1 + - + +
19A ALA* 4.2 3.8 - - - +
21A TYR* 1.3 101.4 - + - +
23A ARG* 1.3 96.0 + - + +
24A PRO* 3.3 6.6 - - - +
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 2.8 20.6 + - + +
22A PHE* 1.3 116.8 + - + +
24A PRO* 1.3 63.5 - - - +
25A THR* 3.1 5.5 + - - +
26A THR* 2.8 35.3 + - + +
27A PHE* 3.7 5.5 - - + -
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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