Contacts of the helix formed by residues 29 - 42 (chain H) in PDB entry 1IBM
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 29 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A C 3.7 24.0 + - - -
590A C 3.2 15.0 - - - -
27H PRO 3.8 1.0 + - - -
28H ALA* 1.3 77.1 - - - +
30H ARG* 1.3 70.1 + - - +
31H PHE* 3.6 7.5 + - - +
32H LYS* 2.8 43.3 + - - +
33H GLU* 3.1 12.7 + - - +
59H LEU* 4.6 0.8 - - - +
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Residues in contact with ARG 30 (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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590A C 2.5 29.9 + - - +
591A U 3.2 37.2 + - - +
643A C 5.6 3.6 - - - +
29H SER* 1.3 71.0 - - - +
31H PHE* 1.3 65.3 + - - +
33H GLU* 2.9 26.5 + - - +
34H GLU* 2.8 27.1 + - + +
50H ARG* 4.9 12.0 - - - +
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Residues in contact with PHE 31 (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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590A C 5.7 0.4 + - - -
642A A 3.8 24.0 - - - -
643A C 4.1 39.1 + - - +
6H ILE* 3.3 33.9 - - + -
29H SER* 3.1 6.4 + - - +
30H ARG* 1.3 78.4 - - - +
32H LYS* 1.3 58.5 + - - +
34H GLU* 2.8 20.5 - - + +
35H ILE* 2.6 45.7 - - + +
85H ARG* 4.8 5.4 - - - -
113H SER* 4.2 1.3 - - - -
118H VAL* 4.0 4.5 - - + -
132H GLU* 5.4 2.5 - - - -
134H ILE* 3.5 34.3 - - + -
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Residues in contact with LYS 32 (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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589A C 4.1 9.7 + - - -
2H LEU* 5.4 4.4 - - - +
5H PRO* 3.6 41.0 - - + +
6H ILE* 4.4 8.1 - - + -
8H ASP* 5.2 3.9 + - - -
9H MET* 3.5 34.3 - - + +
26H VAL* 4.3 7.4 - - + -
27H PRO* 2.8 47.1 + - - +
28H ALA 4.9 0.4 + - - -
29H SER* 2.8 34.3 + - - +
31H PHE* 1.3 71.2 - - + +
33H GLU* 1.3 64.4 + - - +
35H ILE* 2.9 6.7 + - - +
36H LEU* 2.8 27.4 + - - +
59H LEU* 4.2 6.3 - - + -
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Residues in contact with GLU 33 (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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28H ALA* 5.8 1.8 - - + -
29H SER 3.1 8.7 + - - +
30H ARG* 2.9 31.3 + - - +
32H LYS* 1.3 75.8 - - - +
34H GLU* 1.3 56.8 + - - +
36H LEU* 3.0 12.5 + - - +
37H ARG* 2.7 37.8 + - - +
48H TYR* 3.2 24.3 + - - +
50H ARG* 3.3 42.8 + - - +
59H LEU* 4.0 21.3 - - + -
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Residues in contact with GLU 34 (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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642A A 4.8 14.1 - - - +
30H ARG* 2.8 22.6 + - + +
31H PHE* 2.8 22.9 - - + +
33H GLU* 1.3 78.3 - - + +
35H ILE* 1.3 57.8 + - - +
37H ARG* 3.3 23.5 + - - +
38H ILE* 2.8 25.6 - - - +
117H GLY* 5.7 0.7 - - - -
118H VAL* 3.8 33.5 + - + +
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Residues in contact with ILE 35 (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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6H ILE* 3.5 20.0 - - + -
9H MET* 4.2 12.1 - - + -
10H LEU* 4.9 12.8 - - + -
31H PHE* 2.6 65.0 + - + +
32H LYS 2.9 6.2 + - - +
34H GLU* 1.3 73.5 - - + +
36H LEU* 1.3 68.9 + - - +
38H ILE* 2.8 18.9 + - - +
39H LEU* 2.8 35.3 + - + +
111H ILE* 3.7 21.3 - - + -
118H VAL* 4.6 2.5 - - + -
134H ILE* 4.4 13.9 - - + -
135H CYS* 5.2 2.0 - - - -
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H MET* 4.1 19.7 - - + -
13H ILE* 4.9 8.7 - - + -
32H LYS 2.8 20.4 + - - +
33H GLU* 3.2 10.1 - - - +
35H ILE* 1.3 72.8 - - + +
37H ARG* 1.3 57.1 + - - +
39H LEU* 2.7 31.2 + - + +
40H ALA* 2.8 13.2 + - - +
45H ILE* 4.2 15.8 - - + +
48H TYR* 3.9 28.5 - - + -
59H LEU* 3.3 37.7 - - + -
61H VAL* 4.0 23.3 - - + -
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Residues in contact with ARG 37 (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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33H GLU 2.7 16.3 + - - +
34H GLU* 3.3 26.8 + - - +
36H LEU* 1.3 70.3 - - - +
38H ILE* 1.3 60.5 + - + +
40H ALA* 3.6 6.7 + - - +
41H ARG* 3.0 43.2 + - - +
48H TYR* 4.4 12.5 + - + +
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Residues in contact with ILE 38 (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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34H GLU 2.8 31.0 - - - +
35H ILE* 2.8 13.6 + - - +
37H ARG* 1.3 74.1 - - + +
39H LEU* 1.3 67.8 + - - +
40H ALA 3.1 0.2 + - - -
41H ARG* 3.1 21.4 + - - +
42H GLU* 2.7 26.8 + - + +
109H ILE* 3.9 14.4 - - + -
111H ILE* 3.7 24.5 - - + -
118H VAL* 4.0 30.7 - - + +
119H LEU* 4.8 2.9 - - - -
120H THR* 3.8 30.5 - - + -
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Residues in contact with LEU 39 (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 LEU* 5.7 4.0 - - + -
13H ILE* 5.5 8.1 - - + -
35H ILE* 2.8 51.4 - - + +
36H LEU* 2.7 19.8 + - + +
38H ILE* 1.3 72.5 - - + +
40H ALA* 1.3 60.5 + - - +
42H GLU 3.8 0.5 - - - -
43H GLY 3.2 1.9 + - - -
44H PHE* 2.8 56.7 + - + +
45H ILE* 3.7 22.9 - - + -
80H ILE* 4.9 8.7 - - + -
83H ILE* 5.5 3.8 - - + -
109H ILE* 5.7 0.7 - - + -
111H ILE* 3.9 11.0 - - + -
137H VAL* 4.5 19.1 - - + -
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Residues in contact with ALA 40 (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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36H LEU 2.8 10.3 + - - +
37H ARG* 3.7 10.3 - - - +
39H LEU* 1.3 75.8 - - - +
41H ARG* 1.3 55.4 + - - +
43H GLY* 2.4 31.5 + - - -
45H ILE* 3.6 23.9 - - + +
47H GLY* 4.4 13.0 - - - -
48H TYR* 5.1 6.5 - - + -
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Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ARG* 3.0 30.4 + - - +
38H ILE* 3.6 26.6 - - - +
40H ALA* 1.3 78.0 - - - +
42H GLU* 1.3 67.7 + - + +
43H GLY* 3.0 4.5 + - - -
118H VAL 5.2 3.2 + - - -
120H THR* 5.9 0.2 - - - -
123H GLU* 2.7 49.0 + - - -
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Residues in contact with GLU 42 (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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152E ARG* 3.4 28.8 + - - +
38H ILE* 2.7 25.8 + - + +
41H ARG* 1.3 81.1 - - + +
43H GLY* 1.3 62.9 - - - +
44H PHE* 3.5 21.0 + - + -
109H ILE* 3.9 30.6 - - + +
120H THR* 4.2 15.5 + - + +
123H GLU* 4.5 4.3 - - - +
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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
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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