Contacts of the helix formed by residues 113 - 128 (chain D) in PDB entry 1I43
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 ASN 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D VAL* 3.0 25.1 + - - +
84D THR 4.7 5.7 + - - -
87D TYR* 3.3 9.1 + - - -
106D PHE* 3.7 8.9 - - - -
109D GLY* 5.2 3.1 - - - +
112D GLY* 1.3 76.1 - - - +
114D PRO* 1.3 92.8 - - - +
115D THR* 2.7 29.2 + - - +
116D THR* 2.9 28.1 + - - +
117D VAL* 3.0 16.8 + - - +
295D LEU 5.7 1.3 - - - +
297D PRO* 3.0 19.2 - - + +
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Residues in contact with PRO 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 5.6 2.7 - - + -
75C ASP* 5.9 2.2 - - - +
70D ARG 5.0 2.6 - - - +
71D GLY 6.0 0.7 - - - -
72D ILE* 4.2 26.1 - - + +
82D VAL* 3.3 36.1 - - + -
87D TYR* 3.4 17.9 - - + +
106D PHE* 3.4 17.9 - - + -
113D ASN* 1.3 91.2 - - - +
115D THR* 1.3 56.9 + - - +
116D THR 3.1 0.2 - - - -
117D VAL* 2.9 26.6 - - + +
118D VAL* 3.6 12.8 - - - +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 6.1 0.2 - - - -
79D THR* 3.8 17.4 - - - +
80D PRO 3.2 24.2 + - - -
81D VAL* 4.1 4.3 - - - -
82D VAL* 3.5 14.1 - - - +
113D ASN* 2.7 29.1 + - - +
114D PRO* 1.3 75.2 - - - +
116D THR* 1.3 60.3 + - - +
118D VAL* 4.2 2.4 - - - +
297D PRO* 3.4 40.2 + - + -
300D ALA* 3.8 5.2 - - - +
301D TYR* 4.6 6.1 - - - +
304D ILE* 3.5 24.4 - - - +
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Residues in contact with THR 116 (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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112D GLY* 5.8 1.8 - - - -
113D ASN* 2.9 30.3 + - - +
115D THR* 1.3 78.3 - - - +
117D VAL* 1.3 66.8 + - + +
118D VAL 3.1 1.8 - - - -
119D LEU* 2.9 17.3 + - - +
120D GLU* 3.1 23.7 + - + +
134D LEU* 4.7 17.5 - - + +
295D LEU* 4.1 24.0 + - + +
297D PRO* 4.5 2.3 - - - +
300D ALA* 3.9 17.1 - - - +
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Residues in contact with VAL 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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70D ARG 5.1 7.0 - - - +
106D PHE* 3.9 25.4 - - + -
112D GLY* 5.7 1.1 - - - -
113D ASN 3.0 16.5 + - - +
114D PRO* 2.9 28.0 - - + +
116D THR* 1.3 73.6 - - + +
118D VAL* 1.3 54.2 + - + +
120D GLU* 2.8 26.4 + - - +
121D GLU* 2.7 47.5 + - + +
285D ARG* 5.8 0.9 - - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA 4.5 1.2 - - - +
65D GLY* 3.4 20.6 - - - +
66D GLU* 3.5 20.4 - - + +
70D ARG* 3.6 33.0 - - + +
72D ILE* 5.6 0.9 - - + -
79D THR* 3.6 17.7 - - + +
114D PRO 3.6 15.5 - - - +
115D THR 4.2 2.0 - - - +
116D THR 3.1 0.4 - - - -
117D VAL* 1.3 78.3 - - + +
119D LEU* 1.3 57.7 + - - +
121D GLU* 3.4 6.8 + - - +
122D LYS* 2.9 29.5 + - - +
304D ILE* 3.9 18.6 - - + -
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Residues in contact with LEU 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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115D THR 4.8 0.4 - - - +
116D THR* 2.9 12.3 + - - +
118D VAL* 1.3 77.0 - - - +
120D GLU* 1.3 63.8 + - - +
122D LYS* 4.1 6.5 - - + -
123D ILE* 3.1 29.7 + - + +
134D LEU* 3.4 34.5 - - + -
295D LEU* 4.7 1.8 - - + -
300D ALA* 4.0 13.0 - - + +
303D ILE* 3.5 44.2 - - + -
304D ILE* 3.8 26.5 - - + +
307D MET* 3.8 18.8 - - - -
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Residues in contact with GLU 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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116D THR* 3.1 18.2 + - + +
117D VAL* 2.8 30.7 + - - +
119D LEU* 1.3 78.4 - - - +
121D GLU* 1.3 58.9 + - + +
124D SER* 2.8 31.6 + - - -
132D THR* 3.0 34.9 - - - +
133D LEU* 4.0 1.6 - - - +
134D LEU* 3.8 33.9 + - + +
285D ARG* 3.0 30.0 + - - -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR* 5.3 5.2 - - + -
64D ALA* 4.7 1.3 - - - +
65D GLY* 4.3 20.2 + - - +
117D VAL* 2.7 29.6 + - + +
118D VAL* 3.9 5.2 - - - +
120D GLU* 1.3 73.4 - - + +
122D LYS* 1.3 65.0 + - - +
124D SER* 3.4 8.5 + - - -
125D ALA* 3.0 23.0 + - - +
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Residues in contact with LYS 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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60D VAL 4.5 0.9 - - - +
61D ALA* 3.0 22.2 + - - +
62D ILE 2.6 28.7 + - - -
64D ALA* 2.9 38.5 + - + +
66D GLU* 2.7 23.8 + - - -
118D VAL* 2.9 17.3 + - - +
119D LEU* 3.6 13.7 - - + +
120D GLU 3.3 0.2 - - - -
121D GLU* 1.3 74.4 - - - +
123D ILE* 1.3 64.3 + - - +
125D ALA* 3.2 6.4 + - - +
126D LEU* 3.2 20.3 + - - +
304D ILE* 4.3 11.5 + - + +
307D MET* 3.8 26.2 - - + -
308D LYS* 3.3 10.1 - - - +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 3.1 37.6 + - + +
120D GLU 4.2 2.2 - - - +
122D LYS* 1.3 75.7 - - - +
124D SER* 1.3 66.2 + - - +
126D LEU* 3.2 9.1 + - + +
127D GLU* 2.9 29.9 + - + +
132D THR* 3.7 13.9 - - + +
134D LEU* 4.4 6.7 - - + -
242D PRO* 5.8 3.6 - - + -
257D HIS* 5.8 2.2 - - + -
259D ALA* 5.8 0.4 - - + -
263D LEU* 4.2 14.6 - - + -
273D CYS* 3.3 32.5 - - - -
275D SER* 3.7 13.5 - - - +
303D ILE* 5.2 1.8 - - + -
307D MET* 3.9 23.3 - - + -
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Residues in contact with SER 124 (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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120D GLU 2.8 25.1 + - - -
121D GLU* 3.4 10.7 - - - -
123D ILE* 1.3 77.7 - - - +
125D ALA* 1.3 51.6 + - - +
127D GLU 3.5 0.2 + - - -
128D GLY* 2.8 28.8 + - - -
129D ALA* 2.8 27.8 + - - +
130D GLU 5.2 0.9 - - - -
131D SER* 3.5 7.8 - - - -
132D THR* 2.9 31.0 + - - -
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Residues in contact with ALA 125 (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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50D TYR* 4.3 22.4 - - + +
60D VAL* 3.7 10.2 - - + +
64D ALA* 3.7 20.0 - - + -
121D GLU 3.0 13.4 + - - +
122D LYS 3.5 9.2 - - - +
123D ILE 3.2 0.2 - - - -
124D SER* 1.3 74.7 - - - +
126D LEU* 1.3 65.5 + - - +
128D GLY* 2.9 14.5 + - - -
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Residues in contact with LEU 126 (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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57D ASP* 3.6 41.7 - - + +
60D VAL* 3.6 14.6 - - + -
61D ALA* 4.0 7.9 - - + +
122D LYS 3.2 9.3 + - - +
123D ILE* 3.2 9.5 + - - +
125D ALA* 1.3 80.8 - - - +
127D GLU* 1.3 60.0 + - - +
128D GLY 3.4 0.2 + - - -
242D PRO* 4.2 22.0 - - + -
243D LEU* 4.2 7.4 - - + -
246D LYS* 2.7 30.4 + - - +
263D LEU* 5.3 0.2 - - + -
307D MET* 3.7 29.2 - - + -
310D LEU* 3.9 20.9 - - + -
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Residues in contact with GLU 127 (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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123D ILE* 2.9 23.5 + - + +
124D SER 4.2 2.0 - - - +
126D LEU* 1.3 75.5 - - - +
128D GLY* 1.3 63.5 + - - +
129D ALA* 3.1 12.2 + - + +
242D PRO* 3.3 24.5 - - + +
245D GLN 4.5 6.4 - - - +
246D LYS* 4.6 17.5 - - - +
247D ALA 4.7 2.1 + - - -
248D LEU* 3.7 22.4 + - + +
249D ALA* 5.4 0.3 + - - +
255D VAL* 3.6 18.2 - - - +
257D HIS* 2.6 36.2 + - - -
275D SER* 4.0 17.3 - - - +
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Residues in contact with GLY 128 (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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124D SER 2.8 7.8 + - - -
125D ALA* 2.9 13.5 + - - -
126D LEU 3.1 1.0 + - - -
127D GLU* 1.3 79.9 - - - +
129D ALA* 1.3 64.0 + - - +
248D LEU* 4.5 2.5 - - - +
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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
------------------------------------------------------------
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