Contacts of the helix formed by residues 4 - 19 (chain H) in PDB entry 1IBL
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 ASP 4 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A C 3.5 19.6 - - - +
2H LEU* 3.5 1.3 - - - -
3H THR* 1.3 84.8 - - - +
5H PRO* 1.3 56.1 - - - +
6H ILE* 3.1 12.3 + - - +
7H ALA* 3.3 12.9 - - + +
8H ASP* 2.8 32.7 + - - +
85H ARG* 2.6 44.9 + - - -
88H LYS* 4.3 0.3 - - - -
89H PRO* 3.4 21.6 - - + +
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Residues in contact with PRO 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A G 3.7 36.3 - - - +
589A C 3.7 17.3 - - - +
2H LEU* 4.3 14.3 - - + +
3H THR 4.1 1.3 - - - -
4H ASP* 1.3 86.9 - - - +
6H ILE* 1.3 60.3 + - + +
8H ASP* 3.0 10.7 - - + +
9H MET 2.8 24.9 + - - -
32H LYS* 3.4 36.6 - - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 3.1 2.9 + - - +
5H PRO* 1.3 74.2 - - + +
7H ALA* 1.3 67.1 + - - +
9H MET* 3.2 6.8 + - + +
10H LEU* 2.9 40.6 + - + +
31H PHE* 3.3 42.2 - - + -
32H LYS* 3.8 23.8 - - + -
35H ILE* 3.6 27.8 - - + -
85H ARG* 3.6 25.8 - - - +
134H ILE* 4.3 6.7 - - + -
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Residues in contact with ALA 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A G 3.9 16.4 - - - +
877A C 4.0 11.2 - - - +
4H ASP* 3.1 32.4 + - + +
6H ILE* 1.3 78.4 - - - +
8H ASP* 1.3 65.9 + - - +
10H LEU* 3.1 3.7 + - - +
11H THR* 2.8 26.2 + - - -
85H ARG* 3.5 23.3 - - + +
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Residues in contact with ASP 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A G 3.0 33.4 + - - +
826A C 4.7 0.3 - - - +
876A G 5.2 1.6 - - - -
2H LEU* 3.6 21.3 - - + +
4H ASP 2.8 13.9 + - - +
5H PRO* 3.0 15.9 + - + +
7H ALA* 1.3 75.7 - - - +
9H MET* 1.3 55.6 + - - +
11H THR* 2.8 26.9 + - - -
12H ARG* 2.8 42.9 + - - +
27H PRO* 4.2 6.4 - - - +
32H LYS* 5.2 1.0 + - - -
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Residues in contact with MET 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO 2.8 13.7 + - - +
6H ILE* 3.6 16.4 - - + +
8H ASP* 1.3 72.8 + - - +
10H LEU* 1.3 71.8 + - + +
11H THR 2.8 1.4 + - - -
12H ARG* 2.8 21.8 + - - +
13H ILE* 2.8 28.1 + - + +
26H VAL* 4.0 32.1 - - + -
32H LYS* 3.4 46.2 - - + +
35H ILE* 4.3 13.5 - - + -
36H LEU* 3.7 26.5 - - - -
39H LEU* 6.0 1.3 - - + -
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Residues in contact with LEU 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 2.9 31.3 + - + +
7H ALA* 3.5 7.6 - - - +
9H MET* 1.3 79.8 - - + +
11H THR* 1.3 57.4 + - - +
13H ILE* 3.6 4.4 - - + +
14H ARG* 2.9 35.9 + - - +
35H ILE* 5.3 7.4 - - + -
39H LEU* 4.9 11.7 - - + -
83H ILE* 3.2 37.1 - - + +
84H ARG 4.6 0.9 - - - -
85H ARG* 3.4 35.0 - - + +
111H ILE* 6.4 0.2 - - + -
135H CYS* 3.9 29.8 - - + -
137H VAL* 5.6 0.7 - - + -
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Residues in contact with THR 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A G 3.3 16.8 - - - +
826A C 5.0 1.1 - - - -
875A C 3.3 28.3 - - - +
876A G 3.2 27.2 + - - +
7H ALA 2.8 6.8 + - - -
8H ASP* 2.8 13.9 + - - +
9H MET 2.8 0.8 + - - -
10H LEU* 1.3 73.4 - - - +
12H ARG* 1.3 68.4 + - - +
13H ILE 3.0 1.3 - - - -
14H ARG* 2.8 27.2 + - - +
15H ASN* 2.7 30.1 + - - +
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Residues in contact with ARG 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A G 3.2 25.1 + - - -
826A C 3.2 52.9 + - - +
2H LEU* 4.9 3.0 - - - +
8H ASP* 2.8 44.4 + - - +
9H MET* 2.8 7.8 + - - +
11H THR* 1.3 73.1 - - + +
13H ILE* 1.3 64.2 + - - +
15H ASN* 3.8 1.4 - - - +
16H ALA* 3.0 26.1 + - - +
24H THR* 4.3 11.6 + - - +
25H ASP* 3.3 25.9 + - - +
26H VAL* 4.2 8.7 - - + +
27H PRO* 3.5 27.2 - - - +
58H TYR* 4.8 8.1 + - - -
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Residues in contact with ILE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H MET* 2.8 33.3 + - + +
10H LEU* 3.6 7.4 - - + +
12H ARG* 1.3 75.9 - - + +
14H ARG* 1.3 71.0 + - - +
16H ALA* 3.6 3.4 + - - +
17H THR* 3.2 25.0 + - + +
24H THR* 5.2 3.4 - - + -
26H VAL* 5.2 2.5 - - + -
36H LEU* 4.3 4.5 - - + -
39H LEU* 4.1 25.8 - - + -
45H ILE* 5.3 1.1 - - + -
61H VAL* 4.2 27.6 - - + -
63H LEU* 4.2 16.6 - - + -
80H ILE* 3.9 26.7 - - + -
83H ILE* 4.2 10.8 - - + -
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A C 3.0 36.0 + - - +
876A G 3.6 25.6 + - - -
7H ALA 5.4 0.2 + - - -
10H LEU* 2.9 20.9 + - - +
11H THR* 2.8 47.7 + - - +
13H ILE* 1.3 69.9 - - - +
15H ASN* 1.3 66.6 + - - +
17H THR* 2.7 23.5 + - - -
18H ARG* 3.3 25.1 + - - +
80H ILE* 6.1 0.4 - - - -
83H ILE* 3.0 42.4 + - + +
84H ARG* 4.3 9.7 - - - +
85H ARG* 4.8 3.0 - - - +
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Residues in contact with ASN 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A C 2.8 50.9 + - - +
827A U 3.9 13.2 - - - +
874A G 4.1 6.8 + - - -
875A C 3.1 40.1 + - - +
11H THR* 2.7 25.2 + - - +
12H ARG 3.8 0.4 - - - +
14H ARG* 1.3 71.6 - - - +
16H ALA* 1.3 55.9 + - - +
18H ARG* 2.6 39.2 + - - +
19H VAL* 3.5 6.0 + - - +
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A U 5.0 9.4 - - - +
12H ARG 3.0 17.7 + - - +
13H ILE* 4.0 2.5 - - - +
15H ASN* 1.3 75.3 - - - +
17H THR* 1.3 61.8 + - - +
19H VAL* 3.2 7.1 - - - +
20H TYR 3.0 4.2 + - - -
21H LYS* 3.0 46.6 + - + -
24H THR* 4.0 27.6 - - + +
63H LEU* 4.9 3.4 - - + -
65H TYR* 4.3 0.4 - - - -
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Residues in contact with THR 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ILE* 3.2 16.8 + - + +
14H ARG* 2.7 20.4 + - - -
15H ASN 2.8 2.2 + - - -
16H ALA* 1.3 76.4 - - - +
18H ARG* 1.3 67.8 + - - +
19H VAL 3.0 0.4 - - - -
20H TYR* 3.0 14.6 + - - -
63H LEU* 3.6 34.3 - - + -
64H LYS 5.6 1.6 - - - +
65H TYR* 3.4 16.7 - - + +
78H GLN* 2.4 37.9 + - - +
80H ILE* 4.8 11.1 + - + +
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Residues in contact with ARG 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A A 3.6 19.2 + - - +
861A G 5.6 10.1 - - - -
14H ARG* 3.4 26.7 + - + +
15H ASN* 2.6 20.9 + - - +
17H THR* 1.3 90.1 + - - +
19H VAL* 1.3 60.3 + - + -
20H TYR* 3.9 13.0 - - - -
75H ARG* 4.7 4.2 + - - -
78H GLN* 3.9 19.5 - - - +
80H ILE* 3.2 20.0 + - - +
81H HIS* 2.8 29.8 + - - +
83H ILE* 5.8 1.0 - - - +
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Residues in contact with VAL 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A U 3.5 32.1 - - - +
828A A 4.3 2.9 - - - +
859A A 4.2 14.1 - - + +
860A A 4.5 9.6 - - - +
15H ASN 4.4 4.3 - - - +
16H ALA* 3.2 17.9 - - - +
17H THR 3.0 0.2 - - - -
18H ARG* 1.3 83.3 - - + +
20H TYR* 1.3 74.5 - - - +
21H LYS* 3.4 32.7 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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