Contacts of the helix formed by residues 58 - 74 (chain K) 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 PRO 58 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G ALA 5.2 0.4 - - - +
153G HIS* 3.7 38.4 - - + +
56K GLY 3.4 1.5 - - - +
57K THR* 1.3 88.7 - - - +
59K TYR* 1.3 67.7 + - + +
61K ALA* 3.0 5.7 + - - +
62K GLN* 2.9 16.1 + - - +
89K ALA* 5.0 7.4 - - + -
90K GLY* 3.7 28.0 - - - +
93K GLN* 3.9 21.2 - - + +
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Residues in contact with TYR 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G GLU 5.4 0.7 - - - -
149G ARG* 3.3 51.0 + - + +
150G ALA* 3.9 28.7 - - - +
50K TYR* 3.0 28.5 - + - -
57K THR* 3.1 2.6 + - + +
58K PRO* 1.3 80.3 - - - +
60K ALA* 1.3 54.2 + - - +
62K GLN* 2.4 52.6 + - - +
63K LEU* 2.9 44.7 + - + +
93K GLN* 5.9 0.2 - - - -
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Residues in contact with ALA 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K GLY* 4.6 8.1 - - - -
48K ILE* 4.3 1.5 - - - +
50K TYR* 3.3 28.4 - - + -
54K ARG 3.4 1.1 - - - +
55K LYS* 3.3 21.5 - - - +
57K THR* 3.2 23.2 + - + +
59K TYR* 1.3 77.8 - - - +
61K ALA* 1.3 65.0 + - - +
63K LEU* 3.1 6.8 + - - +
64K ALA* 2.8 26.3 + - - +
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Residues in contact with ALA 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K THR* 3.4 37.2 - - + +
55K LYS 4.6 0.4 + - - -
57K THR 3.1 4.6 + - - +
58K PRO 3.0 13.7 + - - +
59K TYR 3.0 0.2 - - - -
60K ALA* 1.3 78.8 - - - +
62K GLN* 1.3 60.9 + - - +
64K ALA* 3.5 3.8 + - - +
65K ALA* 3.0 25.1 + - - +
90K GLY* 3.5 27.8 - - - +
94K ALA* 4.0 6.9 - - + +
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Residues in contact with GLN 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K PRO 2.9 6.2 + - - +
59K TYR* 2.4 46.9 + - + +
61K ALA* 1.3 68.8 - - - +
63K LEU* 1.3 64.9 + - + +
65K ALA* 3.2 2.9 + - - +
66K LEU* 2.8 46.9 + - + +
93K GLN* 3.1 36.2 + - - +
97K ALA* 4.1 14.7 - - + +
100K ALA* 5.9 4.2 - - - +
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Residues in contact with LEU 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K ILE* 3.0 31.4 - - + +
50K TYR* 3.5 34.5 - - + +
59K TYR* 2.9 49.1 + - + +
60K ALA* 3.5 5.2 - - - +
62K GLN* 1.3 77.5 - - + +
64K ALA* 1.3 51.7 + - - +
66K LEU* 3.0 13.8 + - + +
67K ASP* 2.7 33.4 + - - +
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Residues in contact with ALA 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K THR* 4.7 6.1 - - + +
30K VAL* 3.9 8.7 - - + -
43K SER* 3.3 11.2 + - - +
44K SER* 3.6 33.2 - - - +
45K GLY 4.1 0.9 - - - +
48K ILE* 2.9 11.8 - - + +
60K ALA 2.8 20.1 + - - +
61K ALA* 3.7 6.1 - - - +
63K LEU* 1.3 70.0 - - - +
65K ALA* 1.3 66.2 + - - +
67K ASP* 2.8 4.4 + - - +
68K ALA* 2.8 21.8 + - - +
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Residues in contact with ALA 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K VAL* 3.6 16.5 - - + +
61K ALA 3.0 16.2 + - - +
64K ALA* 1.3 75.6 - - - +
66K LEU* 1.3 65.0 + - - +
68K ALA* 3.2 3.3 + - - +
69K ALA* 2.9 21.1 + - - +
94K ALA* 3.9 17.7 - - + +
97K ALA* 3.4 28.0 - - + -
98K LEU* 4.0 16.9 - - + +
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Residues in contact with LEU 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K GLN* 2.8 43.4 + - + +
63K LEU* 3.3 14.8 - - + +
65K ALA* 1.3 72.9 - - - +
67K ASP* 1.3 66.0 + - - +
69K ALA* 3.0 12.6 + - - +
70K LYS* 3.2 36.5 + - - +
97K ALA* 4.2 24.7 - - + +
100K ALA* 5.1 3.8 - - + -
101K SER* 4.2 18.4 - - - +
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Residues in contact with ASP 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K SER* 3.1 17.4 + - - +
47K VAL* 3.3 10.0 - - - +
48K ILE* 4.4 9.2 - - + +
63K LEU 2.7 15.2 + - - +
64K ALA* 2.8 11.2 + - - +
66K LEU* 1.3 73.0 - - - +
68K ALA* 1.3 64.2 + - - +
69K ALA 2.9 0.2 + - - -
70K LYS* 3.3 12.1 + - - +
71K LYS* 3.1 61.3 + - - +
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Residues in contact with ALA 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K VAL* 3.5 30.7 - - + +
32K ILE* 3.6 19.3 - - + +
41K THR* 3.5 6.4 + - - -
42K TRP* 4.7 2.9 - - - -
43K SER* 3.6 15.6 - - - +
64K ALA 2.8 8.6 + - - +
65K ALA 3.4 9.0 - - - +
67K ASP* 1.3 73.3 - - - +
69K ALA* 1.3 65.8 + - - +
71K LYS* 4.6 3.8 - - - -
72K ALA* 3.1 21.5 + - - +
98K LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K ILE* 4.8 0.8 - - - +
65K ALA 2.9 11.9 + - - +
66K LEU* 3.0 9.4 + - + +
67K ASP 2.9 0.6 + - - -
68K ALA* 1.3 72.4 - - - +
70K LYS* 1.3 58.6 + - + +
72K ALA* 2.4 30.0 + - - +
73K MET* 2.7 19.1 + - + +
98K LEU* 4.8 1.8 - - + +
101K SER* 3.6 25.1 - - - -
103K LEU* 3.5 29.6 - - + -
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Residues in contact with LYS 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K LEU* 3.6 33.2 - - - +
67K ASP* 3.7 10.0 - - - +
69K ALA* 1.3 76.6 - - + +
71K LYS* 1.3 58.8 + - + +
73K MET* 2.5 45.1 + - + +
74K ALA* 3.0 11.5 + - - +
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Residues in contact with LYS 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A U 6.2 0.2 - - - -
687A A 3.7 21.2 + - - -
41K THR* 3.7 28.3 - - + +
42K TRP 3.8 22.4 + - - +
47K VAL* 3.8 11.3 - - - +
67K ASP* 3.1 48.6 + - - +
68K ALA* 3.9 1.8 - - - +
69K ALA 3.0 0.2 + - - -
70K LYS* 1.3 80.5 - - + +
72K ALA* 1.3 58.1 + - - +
74K ALA* 3.6 16.6 - - - +
75K TYR* 3.9 8.5 - - - -
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Residues in contact with ALA 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ILE* 3.7 27.8 - - + -
40K ILE* 4.2 7.6 - - + -
41K THR* 3.4 13.9 - - - +
68K ALA 3.1 18.9 + - - +
69K ALA* 2.4 20.9 + - - +
71K LYS* 1.3 67.5 - - - +
73K MET* 1.3 61.2 + - - -
74K ALA 3.1 2.0 - - - -
75K TYR* 3.1 13.3 + - - +
77K MET* 3.0 25.5 + - + +
103K LEU* 5.0 1.6 - - + -
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Residues in contact with MET 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ALA* 2.7 13.6 + - + +
70K LYS* 2.5 44.4 + - + +
72K ALA* 1.3 73.4 - - - +
74K ALA* 1.3 52.3 + - - +
76K GLY* 2.6 28.4 + - - -
77K MET* 3.5 20.8 + - - +
78K GLN* 5.8 0.9 - - - -
101K SER* 4.8 0.7 - - - -
102K GLY* 3.4 41.1 - - - +
103K LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LYS 4.1 6.8 + - - -
13K GLN* 4.6 4.2 + - - -
70K LYS 3.0 7.8 + - - +
71K LYS* 3.6 14.6 - - - +
73K MET* 1.3 79.0 - - - +
75K TYR* 1.3 61.5 + - + +
76K GLY* 3.1 3.8 + - - -
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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