Contacts of the helix formed by residues 90 - 100 (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 GLY 90 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28K THR* 4.1 2.5 - - - -
56K GLY 4.6 0.4 - - - -
58K PRO* 3.7 22.3 - - - +
61K ALA* 3.5 26.4 - - - +
89K ALA* 1.3 72.7 - - - +
91K ARG* 1.3 69.3 + - - +
92K GLU 5.0 0.2 - - - +
93K GLN* 3.1 9.8 + - - +
94K ALA* 2.8 18.5 + - - +
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Residues in contact with ARG 91 (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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21K ILE* 4.8 6.4 - - + +
23K ALA* 3.3 28.5 - - + -
28K THR* 5.2 0.4 - - - -
84K VAL* 3.3 32.1 - - + -
86K GLY 3.6 11.0 + - - +
87K THR* 3.2 37.6 + - - +
88K GLY 3.5 12.0 + - - +
89K ALA 2.7 5.9 + - - -
90K GLY* 1.3 82.6 - - - +
92K GLU* 1.3 66.5 + - - +
93K GLN 2.6 8.7 + - - -
94K ALA* 2.8 10.9 + - - +
95K ILE* 3.2 12.0 + - + +
110K ASP* 3.4 5.9 + - - -
88R LYS* 2.4 44.3 - - - +
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Residues in contact with GLU 92 (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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90K GLY 5.0 0.2 - - - +
91K ARG* 1.3 88.8 + - - +
93K GLN* 1.3 60.7 + - - +
95K ILE* 3.2 25.5 - - - +
96K ARG* 3.2 46.9 + - - +
88R LYS* 3.1 48.6 - - - +
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Residues in contact with GLN 93 (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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58K PRO* 3.9 24.5 - - + +
59K TYR* 5.9 0.2 - - - -
62K GLN* 3.1 50.4 + - - +
90K GLY* 3.2 22.6 - - - +
91K ARG 2.6 6.3 + - - -
92K GLU* 1.3 73.0 - - - +
94K ALA* 1.3 58.8 + - - +
96K ARG* 3.1 32.3 + - - +
97K ALA* 2.8 19.1 + - - +
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Residues in contact with ALA 94 (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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21K ILE* 4.0 23.8 - - + -
28K THR* 4.5 6.7 - - + -
30K VAL* 4.7 2.0 - - + -
61K ALA* 4.0 10.1 - - - +
65K ALA* 3.9 16.6 - - + -
90K GLY 2.8 9.8 + - - +
91K ARG 2.8 11.2 + - - +
93K GLN* 1.3 72.6 + - - +
95K ILE* 1.3 66.4 + - - +
97K ALA* 2.9 9.8 + - - +
98K LEU* 2.8 28.6 + - - +
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Residues in contact with ILE 95 (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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21K ILE* 3.7 22.0 - - + +
82K VAL* 5.0 5.1 - - + +
84K VAL* 3.7 23.3 - - + -
91K ARG* 3.4 13.9 - - + +
92K GLU* 3.2 44.2 - - - +
93K GLN 3.2 0.2 - - - -
94K ALA* 1.3 79.9 - - - +
96K ARG* 1.3 61.7 + - + +
98K LEU* 3.7 5.5 + - - +
99K GLN* 3.0 26.6 + - + +
105K VAL* 4.7 0.3 - - - +
108K ILE* 3.4 37.5 - - + -
88R LYS* 4.1 7.9 - - - +
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Residues in contact with ARG 96 (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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92K GLU* 3.2 38.5 + - - +
93K GLN* 3.1 32.0 + - - +
94K ALA 3.1 0.2 - - - -
95K ILE* 1.3 78.6 - - + +
97K ALA* 1.3 68.9 + - - +
99K GLN* 3.0 21.6 + - - +
100K ALA* 2.9 19.9 + - - +
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Residues in contact with ALA 97 (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* 4.1 20.9 - - + +
65K ALA* 3.4 21.5 - - + -
66K LEU* 4.2 13.6 - - + +
93K GLN* 2.8 14.5 + - - +
94K ALA* 2.9 16.1 + - - +
96K ARG* 1.3 75.3 - - - +
98K LEU* 1.3 57.5 + - - +
100K ALA* 2.6 30.7 + - - +
101K SER* 2.9 9.9 + - - -
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Residues in contact with LEU 98 (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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19K ALA* 3.3 30.3 - - + -
21K ILE* 4.3 12.6 - - + -
30K VAL* 5.3 3.8 - - + -
32K ILE* 4.5 10.1 - - + -
65K ALA* 4.0 27.8 - - + +
68K ALA* 5.4 0.9 - - + -
69K ALA* 4.8 0.9 - - + -
80K VAL* 5.6 2.0 - - + -
82K VAL* 3.6 24.0 - - + -
94K ALA 2.8 18.4 + - - +
95K ILE 4.0 5.2 - - - +
97K ALA* 1.3 72.2 - - - +
99K GLN* 1.3 58.8 + - - +
101K SER* 2.5 25.0 + - - +
103K LEU* 3.3 32.0 - - + +
105K VAL* 3.8 11.2 - - + +
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Residues in contact with GLN 99 (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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95K ILE* 3.0 16.6 - - - +
96K ARG* 3.1 27.3 + - - +
97K ALA 2.7 5.1 + - - -
98K LEU* 1.3 71.2 - - - +
100K ALA* 1.3 59.4 + - - +
101K SER 3.1 13.1 + - - +
103K LEU 4.2 3.7 - - - +
105K VAL* 3.3 30.2 + - + +
108K ILE* 3.9 22.0 - - - +
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Residues in contact with ALA 100 (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* 5.9 3.8 - - - +
66K LEU* 5.1 4.9 - - + +
96K ARG 2.9 9.4 + - - +
97K ALA* 2.6 16.9 + - - +
99K GLN* 1.3 67.5 - - - +
101K SER* 1.3 65.5 + - - +
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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