Contacts of the helix formed by residues 155 - 170 (chain D) in PDB entry 1GUL
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 LEU 155 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 3.6 35.2 - - + -
72D LEU* 4.2 26.9 - - + +
73D HIS* 4.5 13.5 - - + -
76D ALA* 4.0 21.3 - - + -
81D LEU* 2.7 20.7 + - - +
82D PHE* 4.8 7.9 - - + -
92D ILE* 4.2 6.3 - - + -
96D VAL* 3.9 20.9 - - + -
154D SER* 1.3 76.8 - - - +
156D ALA* 1.3 62.6 + - - +
158D VAL* 3.2 5.1 + - - -
159D ILE* 3.2 32.4 + - + +
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Residues in contact with ALA 156 (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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92D ILE* 3.9 13.5 - - + +
95D TYR* 3.8 30.7 - - + -
96D VAL* 3.7 16.4 - - + +
99D THR* 5.3 1.4 + - - -
148D LEU* 4.1 14.5 - - + +
154D SER* 3.0 11.5 + - - +
155D LEU* 1.3 79.5 - - - +
157D ASP* 1.3 61.5 + - - +
159D ILE* 3.5 2.0 + - - +
160D LEU* 3.0 26.2 + - - +
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Residues in contact with ASP 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 3.6 9.3 - - - +
148D LEU* 2.8 30.5 + - - +
152D GLN 3.5 5.7 - - - +
153D LEU* 3.3 22.6 - - + -
154D SER* 2.9 34.2 + - - +
156D ALA* 1.3 76.7 - - - +
158D VAL* 1.3 58.2 + - - +
160D LEU* 3.9 0.3 - - - +
161D LEU* 2.8 31.4 + - - +
184D TYR* 2.6 31.4 + - - +
188D LEU* 3.9 9.0 - - + +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TRP* 3.5 49.5 - - + +
22D VAL* 4.1 15.7 - - + +
25D ALA* 4.0 20.9 - - + -
81D LEU* 5.2 5.8 - - + -
153D LEU* 4.6 13.0 - - + -
154D SER 3.6 13.0 - - - +
155D LEU* 3.2 9.0 + - - +
157D ASP* 1.3 79.3 - - - +
159D ILE* 1.3 53.8 + - + +
161D LEU* 3.5 6.1 - - + +
162D GLN* 2.7 33.6 + - - +
194D ILE* 5.5 3.4 - - + -
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Residues in contact with ILE 159 (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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18D SER* 3.8 28.3 - - - +
22D VAL* 4.4 8.5 - - + -
72D LEU* 4.3 7.9 - - + -
96D VAL* 4.5 14.6 - - + +
99D THR* 3.8 22.2 - - + -
100D LEU* 3.9 23.8 - - + -
103D LEU* 4.8 0.7 - - + -
155D LEU* 3.2 37.1 + - + +
156D ALA 4.1 2.5 - - - +
158D VAL* 1.3 77.9 - - + +
160D LEU* 1.3 54.9 + - - +
162D GLN* 3.5 11.0 - - - +
163D THR* 2.6 40.3 + - - +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D THR* 4.1 17.5 - - + +
102D LEU* 6.0 1.6 - - + -
133D PHE* 4.6 8.7 - - + -
136D PHE* 3.8 49.6 - - + -
148D LEU* 3.8 19.1 - - + -
156D ALA 3.0 18.3 + - - +
157D ASP 3.9 2.7 - - - +
159D ILE* 1.3 74.6 - - - +
161D LEU* 1.3 67.3 + - - +
163D THR* 3.1 3.5 + - + -
164D ILE* 2.8 49.3 + - + +
181D LEU* 4.6 4.7 - - + -
184D TYR* 4.0 15.5 - - + +
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TRP* 3.4 28.7 - - + -
157D ASP 2.8 18.8 + - - +
158D VAL* 3.5 4.9 - - - +
160D LEU* 1.3 78.1 - - - +
162D GLN* 1.3 65.3 + - - +
164D ILE* 3.4 6.0 + - + +
165D LEU* 3.0 47.8 + - + +
184D TYR* 5.2 0.9 - - - -
185D THR* 4.0 23.6 - - + +
188D LEU* 4.0 25.0 - - + +
189D SER* 4.0 15.5 - - - +
194D ILE* 3.9 24.2 - - + -
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Residues in contact with GLN 162 (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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17D GLU* 3.8 22.3 - - - +
18D SER* 2.7 40.5 + - - +
21D TRP* 3.7 40.7 - - + +
103D LEU* 3.8 23.4 - - + +
158D VAL 2.7 20.7 + - - +
159D ILE* 3.5 13.0 - - - +
161D LEU* 1.3 75.1 - - - +
163D THR* 1.3 61.6 + - - +
165D LEU* 3.8 2.4 - - - +
166D ALA* 3.1 26.5 + - + +
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Residues in contact with THR 163 (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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99D THR* 3.4 19.6 - - + +
102D LEU* 4.0 32.5 - - + -
103D LEU* 3.8 30.7 - - + +
106D LEU* 4.8 1.1 - - + -
159D ILE* 2.6 24.2 + - - +
160D LEU* 3.5 5.6 - - + -
162D GLN* 1.3 76.0 - - - +
164D ILE* 1.3 68.1 + - + +
166D ALA* 3.1 6.6 + - - +
167D LEU* 2.9 34.7 + - + +
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Residues in contact with ILE 164 (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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133D PHE* 3.8 25.1 - - + -
160D LEU* 2.8 40.2 + - + +
161D LEU* 3.7 5.6 - - - +
163D THR* 1.3 76.0 - - - +
165D LEU* 1.3 67.9 + - + +
167D LEU* 3.0 11.3 + - - +
168D GLU* 2.7 39.2 + - + +
174D ILE* 4.9 0.4 - - + +
175D LEU* 4.2 25.4 - - + -
181D LEU* 4.4 17.7 - - + -
184D TYR* 4.9 3.6 - - + -
185D THR* 3.9 20.9 - - + +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TRP* 3.8 31.2 - - + -
161D LEU* 3.0 24.9 + - + +
162D GLN 3.8 3.1 - - - +
164D ILE* 1.3 83.0 - - + +
166D ALA* 1.3 62.8 + - - +
168D GLU* 3.3 22.4 + - - +
169D GLU* 3.1 26.4 + - - +
185D THR* 4.1 22.7 - - + -
189D SER* 5.1 2.9 - - - +
198D LEU* 4.1 19.7 - - + -
204D LYS* 5.6 1.8 - - - -
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Residues in contact with ALA 166 (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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13D ARG* 4.9 7.6 - - - +
103D LEU* 5.0 5.4 - - + -
106D LEU* 4.1 23.4 - - + +
162D GLN* 3.1 16.2 + - + +
163D THR* 3.1 11.4 + - - +
165D LEU* 1.3 75.6 - - - +
167D LEU* 1.3 67.1 + - - +
169D GLU* 3.2 31.6 + - - +
170D LYS* 3.7 9.0 + - - +
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Residues in contact with LEU 167 (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 LEU* 4.1 14.4 - - + -
106D LEU* 3.9 21.1 - - + -
124D MET* 3.9 34.5 - - + +
128D ALA* 4.3 4.9 - - + -
133D PHE* 3.8 26.2 - - + -
163D THR* 2.9 31.4 + - + +
164D ILE* 3.3 6.7 - - - +
166D ALA* 1.3 77.3 - - - +
168D GLU* 1.3 52.8 + - - +
170D LYS* 2.6 26.9 + - - +
171D ILE* 2.7 21.2 + - + +
174D ILE* 4.3 20.9 - - + -
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Residues in contact with GLU 168 (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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164D ILE* 2.7 29.6 + - + +
165D LEU* 3.7 24.2 - - - +
166D ALA 3.2 0.2 - - - -
167D LEU* 1.3 78.6 - - - +
169D GLU* 1.3 63.1 + - - +
170D LYS 3.2 0.2 + - - -
171D ILE 3.5 10.3 - - - +
172D PRO* 3.3 36.9 - - + +
174D ILE* 3.7 15.7 - - + -
175D LEU* 3.8 27.3 + - - +
185D THR* 5.2 2.6 - - - +
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Residues in contact with GLU 169 (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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13D ARG* 2.8 45.5 + - - -
165D LEU* 3.1 21.8 + - - +
166D ALA* 3.4 13.9 - - - +
167D LEU 2.9 1.2 - - - -
168D GLU* 1.3 81.7 - - - +
170D LYS* 1.3 64.8 + - + +
172D PRO* 4.8 3.8 - - - +
204D LYS* 4.6 3.8 + - - -
207D PRO* 3.9 16.7 - - + +
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Residues in contact with LYS 170 (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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106D LEU* 4.2 23.5 + - + -
109D HIS* 2.7 36.1 + - + +
110D PRO* 5.5 1.8 - - - +
121D VAL* 4.4 25.9 - - + +
124D MET* 4.5 7.0 - - + -
166D ALA 4.0 11.0 - - - +
167D LEU* 2.6 13.1 + - - +
169D GLU* 1.3 80.2 - - + +
171D ILE* 1.3 69.6 + - + +
172D PRO* 3.3 8.8 - - - +
208D PRO* 6.3 0.4 - - - +
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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
------------------------------------------------------------
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