Contacts of the helix formed by residues 113 - 123 (chain D) 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 SER 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A A 2.6 27.7 + - - -
20D TYR 5.3 0.9 - - - -
21D LEU* 4.4 3.8 - - - -
22D LYS 3.9 9.9 - - - -
23D GLY 3.9 17.3 - - - +
106D TYR* 3.2 16.8 - - - -
111D ALA* 4.0 2.3 - - - +
112D VAL* 1.3 79.0 - - - +
114D ARG* 1.3 60.2 + - - +
115D ARG* 3.4 2.7 + - - +
116D GLN* 3.0 17.0 + - - +
117D ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 4.4 12.6 + - - +
21D LEU* 5.9 2.4 - - + +
67D ILE* 3.7 35.4 + - - +
68D TYR* 4.0 34.6 - - - +
69D GLY* 6.2 0.2 - - - -
98D GLU* 4.3 0.4 + - - -
102D ASP* 5.0 9.3 - - - +
103D ASN* 2.8 40.9 + - - +
106D TYR* 3.6 35.1 + - + -
107D ARG* 3.7 25.5 - - - +
113D SER* 1.3 73.1 - - - +
115D ARG* 1.3 59.8 + - + +
116D GLN 3.1 1.1 - - - -
117D ALA* 3.5 6.2 - - - +
118D ARG* 2.6 36.8 + - - +
196D LEU* 5.6 1.4 - - - +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A G 3.2 44.5 + - - +
408A A 3.9 19.2 + - - +
430A A 5.0 3.4 + - - -
3D ARG 4.8 2.4 + - - -
4D TYR* 4.2 2.9 - - - +
5D ILE* 3.2 34.4 - - - +
6D GLY 3.5 8.9 + - - +
8D VAL* 2.8 33.1 - - - +
21D LEU* 3.7 37.7 + - + +
22D LYS* 5.9 3.2 - - - +
69D GLY* 6.5 1.1 - - - -
113D SER* 3.4 0.6 + - - +
114D ARG* 1.3 79.5 - - + +
116D GLN* 1.3 66.0 + - - +
118D ARG* 3.3 19.4 - - - +
119D GLN* 3.3 4.3 + - - +
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A G 2.9 36.2 + - - +
408A A 3.5 20.9 + - - -
111D ALA* 2.7 14.3 - - + +
112D VAL* 2.6 39.1 + - - +
113D SER* 3.0 19.5 + - - +
115D ARG* 1.3 74.6 - - - +
117D ALA* 1.3 57.7 + - - +
119D GLN* 2.6 31.4 + - + +
120D LEU* 3.1 11.6 + - + +
157D LEU* 3.7 34.7 - - + +
161D ASN* 3.5 1.7 + - - -
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASP* 3.8 15.3 - - - +
105D VAL* 3.8 22.3 - - + +
106D TYR* 4.2 6.1 - - + +
111D ALA* 3.8 13.6 - - + +
113D SER 2.9 21.0 + - - +
114D ARG* 3.2 8.3 + - - +
116D GLN* 1.3 75.3 - - - +
118D ARG* 1.3 64.6 + - - +
120D LEU* 3.0 18.4 + - - +
121D VAL* 3.3 15.3 + - - +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A C 4.3 8.7 + - - -
404A U 3.1 31.7 + - - +
3D ARG* 2.7 56.4 - - - +
69D GLY 4.0 11.1 + - - -
100D ARG* 3.4 24.2 - - - +
102D ASP* 4.2 18.1 + - + +
114D ARG 2.6 20.7 + - - +
115D ARG* 3.3 11.9 - - - +
116D GLN 2.8 2.8 + - - -
117D ALA* 1.3 71.3 - - - +
119D GLN* 1.3 62.0 + - - +
121D VAL* 3.0 16.1 + - - +
122D ARG* 3.2 11.8 + - - +
136D PRO* 3.8 18.5 - - + +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A U 4.9 0.8 + - - -
406A G 3.4 23.4 + - - +
407A G 2.7 36.8 + - - +
436A C 5.0 1.0 - - - +
437A U 3.4 9.8 + - - -
496A A 3.2 20.6 - - - +
115D ARG 3.3 6.3 + - - +
116D GLN* 2.6 17.6 + - + +
118D ARG* 1.3 75.1 - - - +
120D LEU* 1.3 62.7 + - + +
122D ARG* 3.3 6.3 + - - +
123D HIS* 3.0 60.9 + - + +
125D HIS* 6.1 0.2 - - + -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A U 6.4 0.4 - - - -
105D VAL* 4.6 5.8 - - + -
110D PHE* 3.5 14.8 - - + +
111D ALA* 3.4 32.3 - - + -
116D GLN* 3.1 15.0 + - + +
117D ALA* 3.0 11.7 + - - +
119D GLN* 1.3 80.0 - - + +
121D VAL* 1.3 59.1 + - - +
124D GLY 3.7 0.5 + - - -
125D HIS* 3.0 60.2 + - + +
126D ILE* 3.7 17.2 - - + +
157D LEU* 4.4 15.5 - - + -
158D ILE* 4.2 19.3 - - + -
161D ASN* 5.0 1.8 - - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.1 13.2 - - + -
102D ASP* 4.4 20.2 - - - -
105D VAL* 4.5 4.5 - - + -
117D ALA 3.5 13.9 - - - +
118D ARG* 3.0 8.3 + - - +
120D LEU* 1.3 77.2 - - - +
122D ARG* 1.3 60.1 + - - +
123D HIS 3.1 1.1 - - - -
124D GLY* 3.1 13.3 + - - -
126D ILE* 4.1 17.9 - - + -
133D VAL 3.1 20.5 - - - +
134D ASP* 2.9 23.6 - - - -
135D LEU 3.4 20.6 - - - +
136D PRO* 3.6 15.5 - - + -
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A C 3.0 47.4 + - - +
404A U 3.4 31.4 - - - +
439A A 4.6 4.6 + - - +
619A U 4.0 6.5 + - - -
118D ARG 3.2 6.5 + - - +
119D GLN* 3.3 9.6 + - - +
121D VAL* 1.3 79.8 - - - +
123D HIS* 1.3 71.1 + - + +
124D GLY 3.1 2.4 + - - -
134D ASP* 2.5 55.5 + - - +
135D LEU* 4.3 4.2 - - - +
136D PRO* 4.4 9.9 - - + -
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Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A U 6.2 0.4 - - - -
405A U 6.0 1.1 - - - -
437A U 2.8 37.3 + - + +
438A G 3.9 14.6 + - - +
439A A 3.5 28.9 + - - -
496A A 3.8 8.2 + - - -
497A A 5.6 1.6 - - - -
119D GLN* 3.0 54.0 + - + +
120D LEU 3.9 0.2 - - - -
121D VAL 3.1 0.2 - - - -
122D ARG* 1.3 89.1 + - + +
124D GLY* 1.3 64.4 + - - +
125D HIS* 3.1 23.4 + - + +
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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