Contacts of the helix formed by residues 155 - 170 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 3.6 35.2 - - + -
72C LEU* 4.2 26.0 - - + +
73C HIS* 4.5 13.9 - - + -
76C ALA* 4.0 20.9 - - + -
81C LEU* 2.7 22.0 + - + +
82C PHE* 4.8 7.6 - - + -
92C ILE* 4.2 6.3 - - + -
96C VAL* 3.9 20.4 - - + -
154C SER* 1.3 75.3 - - - +
156C ALA* 1.3 64.3 + - - +
158C VAL* 3.2 5.1 + - - -
159C ILE* 3.2 33.4 + - + +
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.9 13.5 - - + +
95C TYR* 3.8 30.7 - - + -
96C VAL* 3.7 16.2 - - + +
99C THR* 5.3 1.2 + - - -
148C LEU* 4.1 13.4 - - + +
149C VAL* 5.4 0.4 - - + -
154C SER* 3.0 11.5 + - - +
155C LEU* 1.3 78.9 - - - +
157C ASP* 1.3 61.8 + - - +
159C ILE* 3.5 1.2 + - - +
160C LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PHE* 3.6 9.6 - - - +
148C LEU* 2.8 29.2 + - - +
149C VAL 5.1 0.2 - - - +
152C GLN 3.5 5.9 - - - +
153C LEU* 3.3 22.5 - - + -
154C SER* 2.9 33.2 + - - +
156C ALA* 1.3 77.3 - - - +
158C VAL* 1.3 59.1 + - - +
160C LEU* 3.9 0.2 - - - +
161C LEU* 2.8 31.6 + - - +
184C TYR* 2.6 31.2 + - - +
188C LEU* 3.9 9.1 - - + +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.5 49.1 - - + +
22C VAL* 4.1 14.4 - - + +
25C ALA* 4.0 21.5 - - + -
81C LEU* 5.2 5.8 - - + -
153C LEU* 4.6 13.7 - - + -
154C SER 3.6 13.5 - - - +
155C LEU* 3.2 9.0 + - - +
157C ASP* 1.3 78.7 - - - +
159C ILE* 1.3 54.6 + - + +
161C LEU* 3.5 6.7 - - + +
162C GLN* 2.7 33.3 + - - +
194C ILE* 5.5 4.0 - - + -
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.8 27.8 - - - +
22C VAL* 4.4 7.9 - - + -
72C LEU* 4.3 8.7 - - + -
96C VAL* 4.5 13.7 - - + +
99C THR* 3.8 22.0 - - + -
100C LEU* 3.9 23.6 - - + +
103C LEU* 4.8 0.4 - - + -
155C LEU* 3.2 39.1 + - + +
156C ALA 4.1 2.5 - - - +
158C VAL* 1.3 78.1 - - + +
160C LEU* 1.3 55.7 + - - +
162C GLN* 3.5 11.0 - - - +
163C THR* 2.6 40.8 + - - +
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Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C THR* 4.1 18.1 - - + +
102C LEU* 6.0 0.9 - - + -
133C PHE* 4.6 9.0 - - + -
136C PHE* 3.8 48.7 - - + -
148C LEU* 3.8 18.4 - - + -
156C ALA 3.0 18.7 + - - +
157C ASP 3.9 2.5 - - - +
159C ILE* 1.3 75.4 - - - +
161C LEU* 1.3 67.0 + - - +
163C THR* 3.1 4.1 + - + -
164C ILE* 2.8 48.8 + - + +
181C LEU* 4.6 4.0 - - + -
184C TYR* 4.0 15.7 - - + +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.4 28.7 - - + -
157C ASP 2.8 19.0 + - - +
158C VAL* 3.5 4.5 - - - +
160C LEU* 1.3 77.6 - - - +
162C GLN* 1.3 65.7 + - - +
164C ILE* 3.7 6.0 - - + +
165C LEU* 3.0 47.7 + - + +
184C TYR* 5.2 0.6 - - + -
185C THR* 4.0 23.8 - - + +
188C LEU* 4.0 24.4 - - + +
189C SER* 4.0 15.7 - - - +
194C ILE* 3.9 24.0 - - + -
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Residues in contact with GLN 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.8 21.7 - - - +
18C SER* 2.7 40.7 + - - +
21C TRP* 3.7 39.8 + - + +
103C LEU* 3.8 22.9 - - + +
158C VAL 2.7 20.9 + - - +
159C ILE* 3.5 12.8 - - - +
161C LEU* 1.3 74.0 - - - +
163C THR* 1.3 62.5 + - - +
165C LEU* 3.6 2.8 + - - +
166C ALA* 3.1 27.0 + - + +
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C THR* 3.4 19.2 - - + +
102C LEU* 4.0 32.1 - - + -
103C LEU* 3.8 30.1 - - + +
106C LEU* 4.8 1.1 - - + -
159C ILE* 2.6 25.4 + - - +
160C LEU* 3.5 5.6 - - + -
162C GLN* 1.3 77.2 - - - +
164C ILE* 1.3 68.1 + - + +
166C ALA* 3.1 6.3 + - - +
167C LEU* 2.9 34.8 + - + +
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 3.8 24.5 - - + -
160C LEU* 2.8 40.4 + - + +
161C LEU* 3.7 6.1 - - - +
163C THR* 1.3 75.4 - - - +
165C LEU* 1.3 69.3 + - + +
167C LEU* 3.0 11.8 + - - +
168C GLU* 2.7 38.1 + - + +
175C LEU* 4.2 26.9 - - + -
181C LEU* 4.4 17.3 - - + -
184C TYR* 4.9 3.6 - - + -
185C THR* 3.9 20.6 - - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.8 32.1 - - + -
161C LEU* 3.0 25.6 + - + +
162C GLN 3.8 3.1 - - - +
164C ILE* 1.3 82.4 - - + +
166C ALA* 1.3 62.5 + - - +
168C GLU* 3.3 21.6 + - - +
169C GLU* 3.1 27.2 + - - +
185C THR* 4.1 22.4 - - + -
189C SER* 5.1 2.5 - - - +
198C LEU* 4.1 19.5 - - + -
204C LYS* 5.6 2.0 - - - -
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 4.9 7.4 - - - +
103C LEU* 5.0 5.2 - - + -
106C LEU* 4.1 23.1 - - + +
162C GLN* 3.1 16.0 + - + +
163C THR* 3.4 11.4 - - - +
165C LEU* 1.3 75.4 - - - +
167C LEU* 1.3 67.0 + - - +
169C GLU* 3.2 31.3 + - - +
170C LYS* 3.7 9.4 + - - +
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 4.1 14.4 - - + -
106C LEU* 3.9 20.2 - - + -
124C MET* 3.9 35.2 - - + +
128C ALA* 4.3 4.5 - - + -
133C PHE* 3.8 26.7 - - + -
163C THR* 2.9 32.1 + - + +
164C ILE* 3.3 6.3 - - - +
166C ALA* 1.3 76.7 - - - +
168C GLU* 1.3 52.8 + - - +
170C LYS* 2.6 26.7 + - - +
171C ILE* 2.7 20.9 + - + +
174C ILE* 4.3 21.5 - - + -
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Residues in contact with GLU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ILE* 2.7 28.3 + - + +
165C LEU* 3.7 24.2 - - - +
166C ALA 3.2 0.2 - - - -
167C LEU* 1.3 79.0 - - - +
169C GLU* 1.3 62.6 + - - +
170C LYS 3.2 0.2 + - - -
171C ILE 3.5 9.9 - - - +
172C PRO* 3.3 37.3 - - + +
174C ILE* 3.7 15.7 - - + -
175C LEU* 3.8 26.5 + - - +
185C THR* 5.2 3.4 - - - +
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 2.8 44.6 + - - -
165C LEU* 3.1 21.9 + - - +
166C ALA* 3.4 14.2 - - - +
167C LEU 2.9 1.0 - - - -
168C GLU* 1.3 81.7 - - - +
170C LYS* 1.3 62.3 + - + +
172C PRO* 4.8 3.5 - - - +
204C LYS* 4.6 3.8 + - - -
207C PRO* 3.9 16.3 - - + +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 4.2 24.2 + - + -
109C HIS* 2.7 36.7 + - + +
110C PRO* 5.5 2.0 - - - +
121C VAL* 4.4 25.9 - - + +
124C MET* 4.5 7.6 - - + -
166C ALA 4.0 10.8 - - - +
167C LEU* 2.6 13.3 + - - +
169C GLU* 1.3 81.0 - - + +
171C ILE* 1.3 68.6 + - + +
172C PRO* 3.3 8.8 - - - +
208C PRO* 6.3 0.6 - - - +
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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