Contacts of the helix formed by residues 114 - 129 (chain D) in PDB entry 2IYL
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D GLY 3.4 1.2 - - - -
113D VAL* 1.3 74.4 - - - +
115D LYS* 1.3 50.5 + - - -
116D THR 3.6 1.8 - - - -
117D THR* 3.8 0.5 - - - -
118D THR* 2.4 44.5 + - - -
227D VAL* 4.1 2.5 - - - -
1001D GDP 2.7 51.4 + - - -
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Residues in contact with LYS 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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107D VAL* 3.9 19.6 - - + +
108D VAL* 3.6 6.5 - - - +
109D GLY* 3.2 43.8 + - - +
110D VAL 4.3 5.1 + - - +
111D ASN* 3.2 27.1 + - - +
113D VAL* 3.8 3.7 - - + -
114D GLY* 1.3 71.9 - - - +
116D THR* 1.3 64.4 + - - +
118D THR* 3.2 2.8 + - - -
119D ILE* 3.0 28.1 + - - +
139D ASP* 4.3 4.8 + - - -
191D ASP* 3.9 10.9 + - - +
192D THR* 3.0 38.5 + - - +
193D ALA 3.8 1.6 - - - -
194D GLY* 3.8 1.8 - - - +
227D VAL* 4.2 11.3 - - + +
1001D GDP 2.8 21.9 + - - +
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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
----------------------------------------------------------
115D LYS* 1.3 71.3 + - - +
117D THR* 1.3 62.9 + - - +
119D ILE* 3.3 7.8 + - - +
120D ALA* 3.0 21.8 + - - +
139D ASP* 5.1 4.7 + - - -
148D GLN* 3.7 31.7 - - + +
149D LEU* 3.7 33.4 - - + +
152D TRP* 4.2 1.8 - - + -
191D ASP* 3.6 18.4 + - - +
1001D GDP 2.9 26.6 + - - -
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Residues in contact with THR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLY 4.0 3.8 - - - -
115D LYS 3.4 0.2 - - - -
116D THR* 1.3 70.5 - - - +
118D THR* 1.3 60.1 + - - +
120D ALA* 3.4 6.5 + - - +
121D LYS* 3.0 41.8 + - + +
148D GLN* 5.6 1.4 + - - +
152D TRP* 4.2 22.5 + - + +
284D GLU 3.9 21.3 - - - +
1001D GDP 2.4 61.2 + - + +
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Residues in contact with THR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D VAL* 5.6 0.2 - - + -
114D GLY 2.4 27.3 + - - -
115D LYS 3.2 4.5 + - - -
117D THR* 1.3 74.5 - - - +
119D ILE* 1.3 54.6 + - + +
121D LYS* 3.1 12.0 + - - +
122D LEU* 2.7 40.0 + - + +
227D VAL* 3.9 12.2 - - + +
253D ILE* 3.5 40.8 - - + -
255D THR* 3.3 22.0 - - - +
289D LEU* 4.4 7.6 - - + +
1001D GDP 4.9 2.1 + - - -
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Residues in contact with ILE 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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107D VAL* 3.8 33.0 - - + -
115D LYS 3.0 17.0 + - - +
116D THR* 3.3 7.4 + - - +
118D THR* 1.3 76.3 - - - +
120D ALA* 1.3 56.9 + - - +
122D LEU* 3.1 9.9 + - + +
123D GLY 2.8 26.9 + - - -
135D PHE* 3.4 30.8 - - + -
149D LEU* 3.8 15.0 - - + -
189D PHE* 3.9 11.0 - - + +
190D VAL 4.3 0.4 - - - -
191D ASP* 3.5 51.4 - - + +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D THR 3.0 11.0 + - - +
117D THR 3.4 9.4 - - - +
119D ILE* 1.3 78.6 - - - +
121D LYS* 1.3 61.5 + - + +
123D GLY 3.4 0.5 + - - -
124D ARG* 3.0 19.5 + - - +
135D PHE* 4.0 11.2 - - - -
149D LEU* 4.7 0.4 - - + +
152D TRP* 3.3 52.0 - - + -
156D LEU* 3.3 13.5 - - + +
286D PRO* 5.4 1.8 - - + -
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D THR* 3.0 33.7 + - + +
118D THR* 3.5 10.8 + - - +
120D ALA* 1.3 76.8 - - + +
122D LEU* 1.3 58.4 + - - +
124D ARG* 3.6 2.1 - - - +
125D TYR* 3.0 30.3 + - - +
152D TRP* 6.4 0.2 - - + -
255D THR* 5.8 0.4 - - - +
281D GLY* 3.7 6.9 - - - -
283D GLY 2.8 28.8 + - - -
284D GLU 4.5 0.2 - - - -
285D GLY 3.4 14.4 - - - -
286D PRO* 3.4 35.1 - - + +
288D ASP 2.8 20.5 + - - -
289D LEU* 3.8 29.6 - - + +
1001D GDP 3.3 20.6 + - - -
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D VAL* 4.7 9.4 - - + -
118D THR* 2.7 25.4 + - + +
119D ILE* 3.4 12.8 - - - +
121D LYS* 1.3 70.7 - - - +
123D GLY* 1.3 60.4 + - - +
125D TYR* 3.4 2.2 + - - +
126D TYR* 2.9 42.6 + - + -
189D PHE* 3.7 33.0 - - + -
225D TRP* 4.1 12.3 - - + -
253D ILE* 3.8 21.5 - - + -
279D PHE* 3.6 31.4 - - + -
289D LEU* 3.6 22.2 - - + +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE 2.8 17.7 + - - -
120D ALA 3.7 2.9 - - - -
122D LEU* 1.3 72.6 - - - +
124D ARG* 1.3 55.8 + - - +
126D TYR 3.8 0.2 - - - -
127D GLN* 2.8 34.1 + - - +
133D VAL* 3.9 11.3 - - - +
135D PHE* 3.8 9.8 - - - -
158D ILE* 3.7 25.1 - - - +
189D PHE* 4.5 0.6 - - - -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ALA 3.0 17.3 + - - +
121D LYS 3.6 4.5 - - - +
123D GLY* 1.3 75.4 - - - +
125D TYR* 1.3 59.1 + - - +
127D GLN* 3.4 14.1 - - - +
128D ASN* 2.9 52.2 + - - +
155D ARG* 5.3 4.2 - - - +
156D LEU* 3.5 31.9 - - + +
158D ILE* 4.4 1.0 - - - +
286D PRO* 3.8 29.3 - - + +
287D ASP* 3.1 40.6 + - - +
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Residues in contact with TYR 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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97D PRO 5.9 0.3 - - - -
98D VAL 4.5 8.1 + - - -
121D LYS 3.0 18.0 + - - +
122D LEU* 3.7 5.8 - - - +
124D ARG* 1.3 78.7 - - - +
126D TYR* 1.3 87.3 + + - +
128D ASN* 3.3 8.3 + - + +
129D LEU* 3.2 55.0 + - + +
279D PHE* 3.8 28.0 - + - -
289D LEU* 4.7 14.4 - - + -
291D PRO* 3.7 33.9 - - + +
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Residues in contact with TYR 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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98D VAL 2.8 29.6 + - - -
99D GLU* 3.6 14.8 - - - -
100D PRO* 3.3 27.9 - - + +
122D LEU* 2.9 33.3 + - + +
125D TYR* 1.3 93.5 - + - +
127D GLN* 1.3 65.5 + - - +
129D LEU* 3.1 16.7 + - + +
130D GLY 3.4 0.3 + - - -
131D LYS* 3.1 28.7 + - + +
133D VAL* 3.8 8.3 - - + -
187D LEU* 3.5 23.6 - - + -
189D PHE* 3.6 26.0 - + - -
225D TRP* 4.1 2.2 - + - -
279D PHE* 3.3 26.9 - + - -
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Residues in contact with GLN 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 GLY 2.8 28.5 + - - +
124D ARG* 3.4 11.8 - - - +
126D TYR* 1.3 73.9 - - - +
128D ASN* 1.3 69.3 + - - +
130D GLY* 3.1 12.6 + - - -
131D LYS 3.4 18.5 + - - +
133D VAL* 3.9 7.0 - - + +
156D LEU* 3.2 47.5 + - - +
157D SER* 4.5 4.6 + - - -
158D ILE* 3.7 15.4 - - + +
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Residues in contact with ASN 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 ARG* 2.9 51.3 + - - +
125D TYR* 3.6 7.4 - - + +
126D TYR 3.2 0.2 - - - -
127D GLN* 1.3 80.3 - - - +
129D LEU* 1.3 65.9 + - + +
130D GLY 3.2 1.3 + - - -
287D ASP* 4.1 5.7 + - - -
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Residues in contact with LEU 129 (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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98D VAL 5.7 0.7 - - - +
99D GLU* 5.7 1.8 - - - +
125D TYR* 3.2 49.9 + - + +
126D TYR* 3.1 19.8 + - + +
128D ASN* 1.3 80.8 - - + +
130D GLY* 1.3 58.4 + - - -
131D LYS* 3.4 13.0 + - + +
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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
------------------------------------------------------------
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