Contacts of the helix formed by residues 6 - 27 (chain A) in PDB entry 5IVH
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 1.3 77.9 - - - +
7A LEU* 1.3 53.1 + - - -
8A MET 3.4 0.9 - - - -
9A GLU* 3.2 25.7 + - - +
10A LYS* 2.4 63.6 + - - +
100A PHE 5.0 6.1 + - - -
101A ILE* 4.4 6.0 + - - +
459A ILE 5.8 0.2 + - - -
462A SER* 4.7 8.0 + - - -
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Residues in contact with LEU 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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5A VAL 2.6 16.1 + - - +
6A SER* 1.3 71.2 - - - +
8A MET* 1.3 68.4 + - - +
10A LYS* 3.5 28.8 - - + +
11A LEU* 3.3 18.9 + - - +
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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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5A VAL* 2.8 48.6 - - + +
7A LEU* 1.3 77.6 - - - +
9A GLU* 1.3 78.1 + - + +
11A LEU* 3.6 5.2 + - - +
12A LYS* 3.3 21.1 + - + +
464A ARG* 4.1 25.1 - - + +
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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
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5A VAL* 5.2 0.2 - - - -
6A SER* 3.5 21.9 + - - +
8A MET* 1.3 101.5 - - - +
10A LYS* 1.3 57.5 + - - +
11A LEU 3.2 1.6 - - - -
12A LYS* 3.3 20.4 - - + -
13A TRP* 2.3 40.4 + - + +
101A ILE* 3.6 10.3 - - + -
459A ILE* 2.8 34.0 - - + +
462A SER* 2.7 26.0 + - - -
464A ARG* 4.1 8.7 + - - +
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Residues in contact with LYS 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 SER* 2.4 53.3 + - - +
7A LEU* 3.5 37.5 - - + +
8A MET 3.4 0.2 - - - -
9A GLU* 1.3 67.8 - - - +
11A LEU* 1.3 56.2 + - - +
13A TRP* 3.8 1.9 - - - +
14A LYS* 2.9 29.8 + - - +
101A ILE* 2.4 53.2 + - + +
102A THR* 4.0 14.7 + - - +
103A GLY* 4.7 1.8 - - - +
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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
----------------------------------------------------------
7A LEU 3.3 8.3 + - - +
8A MET 3.9 7.9 - - - +
9A GLU 3.2 0.2 - - - -
10A LYS* 1.3 75.0 - - - +
12A LYS* 1.3 57.0 + - - +
14A LYS* 3.4 25.8 + - - +
15A ILE* 2.7 63.3 + - + +
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Residues in contact with LYS 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* 3.3 13.0 + - + +
9A GLU* 2.9 26.6 + - + +
11A LEU* 1.3 77.6 - - - +
13A TRP* 1.3 64.6 + - - +
15A ILE* 2.7 20.0 + - - -
16A LYS* 2.7 30.2 + - + +
459A ILE* 6.3 0.4 - - + +
464A ARG* 3.4 38.4 - - - +
483A LEU* 6.3 1.6 - - + -
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Residues in contact with TRP 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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9A GLU* 2.3 31.6 + - + +
10A LYS 3.8 0.4 - - - +
12A LYS* 1.3 66.6 - - - +
14A LYS* 1.3 53.2 + - - +
16A LYS* 2.8 4.0 + - + +
17A CYS* 2.6 62.0 + - - -
99A ASP* 4.9 4.8 + - - -
100A PHE* 3.7 28.7 - + - -
101A ILE* 3.7 34.8 - - + -
146A ASP* 4.1 13.9 + - - -
147A MET* 4.7 2.7 - - - -
456A PRO* 3.5 36.3 - - + -
482A GLN* 3.4 33.2 - - + -
483A LEU* 3.7 29.6 - - + -
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Residues in contact with LYS 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 LYS 2.9 19.7 + - - +
11A LEU* 3.4 26.9 - - - +
13A TRP* 1.3 77.2 - - - +
15A ILE* 1.3 63.3 + - - +
16A LYS 3.1 4.9 + - - -
17A CYS* 3.3 7.2 + - + +
18A ILE* 3.1 46.9 + - + +
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Residues in contact with ILE 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 LEU* 2.7 49.0 + - + +
12A LYS* 2.7 14.9 + - - +
14A LYS* 1.3 77.8 - - - +
16A LYS* 1.3 70.7 + - - +
18A ILE* 4.6 12.1 - - + +
19A GLU* 4.9 5.4 + - - +
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Residues in contact with LYS 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 LYS* 2.7 33.2 + - + +
13A TRP* 3.7 3.8 - - - +
15A ILE* 1.3 85.7 - - - +
17A CYS* 1.3 65.0 + - - +
18A ILE 3.4 0.7 - - - +
19A GLU* 3.7 23.0 + - + +
20A ASN* 3.5 11.1 + - - +
482A GLN* 3.0 37.7 + - - +
483A LEU* 4.1 28.5 - - + -
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Residues in contact with CYS 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 TRP* 2.6 56.5 + - - +
14A LYS* 3.3 8.0 + - + +
16A LYS* 1.3 74.1 - - - +
18A ILE* 1.3 59.3 + - + +
19A GLU 3.3 0.4 - - - -
20A ASN* 3.4 4.7 + - - +
21A LYS* 3.0 24.3 + - - +
146A ASP* 5.4 1.8 - - - -
482A GLN* 3.2 17.0 + - - +
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Residues in contact with ILE 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 LYS* 3.1 37.6 + - + +
15A ILE* 4.9 9.2 - - + -
17A CYS* 1.3 76.3 - - + +
19A GLU* 1.4 60.3 + - - +
21A LYS* 3.5 11.8 - - + +
22A PHE* 3.0 46.1 + - + -
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Residues in contact with GLU 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 ILE 4.9 3.6 - - - +
16A LYS* 3.7 33.2 + - + +
17A CYS 3.3 0.2 - - - -
18A ILE* 1.4 74.0 - - - +
20A ASN* 1.3 56.5 + - - +
21A LYS 2.9 1.8 - - - -
22A PHE* 2.6 37.9 + - - +
23A LEU* 2.6 34.5 + - + +
482A GLN 5.4 5.8 - - - +
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Residues in contact with ASN 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 LYS 3.5 1.9 + - - +
17A CYS 3.4 5.2 + - - +
19A GLU* 1.3 80.4 - - - +
21A LYS* 1.3 58.1 + - - +
23A LEU* 4.4 9.6 - - - +
24A ASN* 2.9 43.8 + - - +
145A ARG* 4.5 4.2 + - - +
146A ASP* 3.7 24.4 + - - +
480A TRP* 4.7 7.9 - - - +
482A GLN* 3.3 47.1 + - + +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A CYS 3.0 13.3 + - - +
18A ILE* 3.5 18.6 - - + +
19A GLU 2.9 1.0 - - - -
20A ASN* 1.3 79.8 + - - +
22A PHE* 1.3 68.2 + - + +
24A ASN* 4.2 2.7 - - - +
25A TYR* 3.4 27.6 + - + +
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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 ILE* 3.0 35.2 + - + +
19A GLU* 2.6 26.5 + - - +
21A LYS* 1.3 79.1 - - + +
23A LEU* 1.3 56.0 + - - +
25A TYR* 4.5 7.2 - + + +
26A ARG* 3.3 34.4 + - + +
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Residues in contact with LEU 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 GLU* 2.6 33.8 + - + +
20A ASN* 4.4 6.5 - - - +
22A PHE* 1.3 73.6 - - - +
24A ASN* 1.3 58.7 + - - +
25A TYR 3.3 0.2 - - - -
26A ARG* 3.2 28.1 + - - +
27A LEU* 2.8 65.3 + - + +
50A VAL* 4.3 11.2 - - + -
480A TRP* 4.1 29.2 - - + +
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Residues in contact with ASN 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 ASN* 2.9 30.5 + - - +
21A LYS* 4.2 3.4 - - - +
23A LEU* 1.3 76.8 - - - +
25A TYR* 1.3 57.0 + - - +
27A LEU* 3.3 11.1 + - - +
28A THR* 2.6 33.9 + - - -
47A ARG* 3.9 10.2 + - - +
91A HIS* 6.1 0.8 + - - -
145A ARG* 2.3 44.0 + - - +
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Residues in contact with TYR 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 LYS* 3.4 19.8 + - + +
22A PHE* 4.5 7.9 - + + +
23A LEU 3.3 0.4 - - - -
24A ASN* 1.3 80.1 - - - +
26A ARG* 1.3 74.8 + - + +
28A THR* 3.0 27.3 + - - +
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Residues in contact with ARG 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* 3.3 23.1 + - + +
23A LEU* 3.2 28.2 + - + +
25A TYR* 1.3 90.2 - - + +
27A LEU* 1.3 61.5 + - - +
28A THR 3.2 7.0 + - - +
48A LEU* 4.4 6.8 - - - +
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Residues in contact with LEU 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 LEU* 2.8 67.5 + - + +
24A ASN* 3.7 11.7 - - - +
25A TYR 3.2 0.2 - - - -
26A ARG* 1.3 73.2 - - - +
28A THR* 1.3 61.7 + - - +
47A ARG* 3.3 8.6 - - + +
48A LEU* 2.9 66.4 + - + +
49A THR* 4.0 16.2 - - - +
50A VAL* 4.1 5.8 - - + +
145A ARG* 5.4 7.2 - - - +
151A ASP* 5.5 3.6 - - - +
480A TRP* 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