Contacts of the helix formed by residues 8 - 25 (chain H) in PDB entry 2IVB
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 ARG 8 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 4.4 21.5 + - + -
90E THR* 5.0 12.6 + - - +
7H ASN* 1.3 75.5 + - - +
9H ASN* 1.3 73.5 + - - +
10H ILE 3.2 1.1 + - - -
11H ARG* 3.3 7.5 + - - +
12H LEU* 3.0 44.4 + - + +
50H GLN* 6.0 0.4 - - - +
80H LEU* 3.5 42.5 - - + +
82H GLY* 2.9 30.5 + - - +
83H CYS 4.4 1.2 - - - -
84H ILE 2.9 21.6 + - - -
85H ASP* 2.9 31.8 + - - +
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Residues in contact with ASN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 5.8 1.6 + - - -
7H ASN* 2.9 25.5 + - - +
8H ARG* 1.3 89.9 + - - +
10H ILE* 1.3 55.0 + - + +
12H LEU* 4.3 10.7 - - - +
13H ASP* 2.7 49.2 + - - +
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Residues in contact with ILE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ASP* 4.1 26.7 - - + +
5H GLN* 3.4 23.1 - - - +
7H ASN* 4.0 15.7 - - - +
8H ARG 3.2 1.0 + - - -
9H ASN* 1.3 77.4 - - + +
11H ARG* 1.3 57.8 + - + +
13H ASP* 3.6 7.1 - - - +
14H LEU* 3.2 24.9 + - - +
74H LEU* 3.7 38.5 - - + +
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Residues in contact with ARG 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLN* 4.4 20.9 - - + +
7H ASN 4.7 0.2 + - - -
8H ARG* 3.3 9.1 + - - +
10H ILE* 1.3 78.4 - - + +
12H LEU* 1.4 61.1 + - + +
14H LEU* 3.5 11.2 + - - +
15H ALA* 3.0 24.6 + - - +
46H ALA 2.9 22.4 + - - -
47H LEU 4.6 1.4 + - - +
49H GLY* 3.8 27.5 - - - +
51H GLN 2.7 26.5 + - - -
74H LEU* 3.1 38.1 + - - -
75H LEU* 3.9 21.7 + - - +
77H MET* 2.8 30.5 + - - +
79H PRO* 4.0 13.1 - - + +
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ARG* 3.0 55.5 + - + +
9H ASN* 4.0 10.5 - - - +
11H ARG* 1.4 73.7 - - + +
13H ASP* 1.3 66.7 + - - +
15H ALA* 3.2 4.9 + - - +
16H ASP* 3.1 28.1 + - - +
48H LEU 3.6 23.1 - - - +
49H GLY* 4.8 2.0 - - - +
50H GLN* 3.9 15.0 - - - +
82H GLY 4.6 4.0 - - - +
83H CYS* 5.3 7.4 - - + +
6I ILE* 4.7 13.5 - - + +
7I ASN* 5.9 2.9 - - + +
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Residues in contact with ASP 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ASN* 2.7 33.0 + - - +
10H ILE* 3.6 7.3 - - - +
12H LEU* 1.3 74.4 - - - +
14H LEU* 1.3 60.9 + - - +
16H ASP* 3.4 15.3 + - - +
17H ALA* 3.1 19.4 + - - +
7I ASN* 5.3 2.3 + - - -
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ILE 3.2 14.1 + - - +
11H ARG* 3.6 17.0 - - - +
12H LEU 3.2 0.4 - - - -
13H ASP* 1.3 72.6 - - - +
15H ALA* 1.3 59.1 + - - +
17H ALA* 3.0 13.1 + - + +
18H ILE* 2.8 44.5 + - + +
47H LEU 5.5 0.4 - - - +
67H LEU* 4.8 4.0 - - + -
71H SER* 3.4 49.1 - - - +
74H LEU* 3.9 22.4 - - + -
75H LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ARG 3.0 13.6 + - - +
12H LEU* 3.2 11.2 + - - +
14H LEU* 1.3 77.0 - - - +
16H ASP* 1.3 56.3 + - - +
18H ILE* 3.4 4.9 + - - +
19H LEU* 2.9 35.0 + - - +
47H LEU 3.2 26.9 - - - +
48H LEU* 3.8 17.9 - - + -
6I ILE* 4.1 15.0 - - + -
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Residues in contact with ASP 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 3.1 15.8 + - - +
13H ASP* 3.6 16.1 - - - +
14H LEU 3.3 0.2 - - - -
15H ALA* 1.3 78.1 - - - +
17H ALA* 1.3 62.3 + - - +
19H LEU* 3.3 9.8 + - - +
20H LEU* 3.1 22.5 + - - +
5I GLN* 4.9 5.6 + - - +
6I ILE* 4.2 12.1 - - - +
7I ASN* 2.9 44.7 + - - +
10I ILE* 4.0 26.1 - - + +
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Residues in contact with ALA 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ASP 3.1 9.2 + - - +
14H LEU* 3.0 19.4 + - + +
16H ASP* 1.3 76.4 - - - +
18H ILE* 1.3 63.4 + - - +
20H LEU* 3.2 8.4 + - - +
21H SER* 3.1 22.9 + - - -
67H LEU* 5.4 4.3 - - + -
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Residues in contact with ILE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 2.8 34.3 + - + +
15H ALA* 3.6 6.3 - - - +
17H ALA* 1.3 76.5 - - - +
19H LEU* 1.3 64.9 + - + +
21H SER* 3.4 7.0 + - - -
22H LYS* 2.9 30.0 + - + +
47H LEU* 3.9 52.5 - - + +
48H LEU* 6.1 0.2 - - + -
65H LEU* 3.6 20.7 - - + +
67H LEU* 3.9 30.7 - - + -
75H LEU* 4.0 11.7 - - + -
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ALA 2.9 22.7 + - - +
16H ASP* 3.8 8.5 - - - +
17H ALA 3.2 0.2 - - - -
18H ILE* 1.3 79.6 - - + +
20H LEU* 1.3 60.7 + - - +
22H LYS* 3.7 11.9 - - + +
23H ALA* 2.9 29.5 + - - +
29H PHE* 3.8 32.3 - - + -
48H LEU* 4.1 12.1 - - + -
3I GLN* 4.8 0.7 - - - +
4I SER 3.5 25.8 - - - +
5I GLN* 4.3 12.1 - - - +
6I ILE* 4.0 37.2 - - + +
77I MET* 4.7 5.3 - - + +
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ASP 3.1 13.3 + - - +
17H ALA* 3.2 9.6 + - - +
19H LEU* 1.3 75.0 - - - +
21H SER* 1.3 53.4 + - - +
23H ALA* 3.1 7.0 + - + +
24H LYS* 2.8 53.6 + - + +
5I GLN* 5.5 1.3 + - - -
70I ASP* 3.9 25.1 - - + +
73I LEU* 4.4 18.6 - - + -
74I LEU* 4.3 28.3 - - + -
77I MET* 5.6 2.2 - - - -
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Residues in contact with SER 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ALA 3.1 13.8 + - - -
18H ILE* 3.6 10.1 - - - -
20H LEU* 1.3 77.4 - - - +
22H LYS* 1.3 53.2 + - - +
24H LYS* 3.3 9.3 + - - +
25H LYS* 2.8 55.4 + - - +
65H LEU* 2.7 36.7 + - - -
67H LEU* 5.1 2.7 - - - -
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Residues in contact with LYS 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 4.4 2.8 + - - -
18H ILE* 2.9 19.5 + - + +
19H LEU* 3.7 11.8 - - + +
21H SER* 1.3 75.1 + - - +
23H ALA* 1.3 57.6 + - - +
25H LYS 3.4 0.5 + - - -
26H ASP* 2.9 23.0 + - - -
27H LEU* 2.9 36.0 + - + +
28H SER 3.7 1.8 - - - -
29H PHE* 3.5 61.5 - - + +
32H ILE* 3.6 19.1 - - + -
65H LEU* 3.7 15.6 - - + +
2I ILE 4.0 8.3 + - - -
3I GLN* 2.6 32.3 + - - +
4I SER 5.1 1.0 - - - +
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU 2.9 19.1 + - - +
20H LEU* 3.4 6.5 - - + +
22H LYS* 1.3 72.5 - - - +
24H LYS* 1.3 67.3 + - - +
26H ASP* 3.0 15.8 + - - +
3I GLN* 3.7 31.2 + - + +
73I LEU* 3.9 30.8 - - + +
77I MET* 4.3 12.1 - - + -
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Residues in contact with LYS 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 2.8 41.9 + - + +
21H SER* 3.6 8.7 - - - +
23H ALA* 1.3 73.1 - - - +
25H LYS* 1.3 66.2 + - + +
26H ASP* 3.4 2.3 + - - +
70I ASP* 3.0 36.2 + - - +
73I LEU* 3.6 19.9 - - + +
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Residues in contact with LYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 2.8 41.8 + - - +
22H LYS 4.1 0.2 - - - +
24H LYS* 1.3 80.9 - - + +
26H ASP* 1.3 70.0 + - - +
27H LEU* 3.2 32.7 - - + +
64H LYS 3.4 26.0 - - - +
65H LEU* 3.8 3.1 + - - -
66H ASP* 3.4 31.0 + - - +
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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
------------------------------------------------------------
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