Contacts of the helix formed by residues 155 - 170 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 3.6 35.0 - - + -
72F LEU* 4.2 26.7 - - + +
73F HIS* 4.5 13.0 - - + -
76F ALA* 4.0 21.5 - - + -
81F LEU* 2.7 23.0 + - + +
82F PHE* 4.8 7.4 - - + -
92F ILE* 4.2 6.3 - - + -
96F VAL* 3.9 20.0 - - + -
154F SER* 1.3 73.9 - - - +
156F ALA* 1.3 63.8 + - - +
158F VAL* 3.2 6.4 + - + -
159F ILE* 3.2 32.9 + - + +
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ILE* 3.9 12.4 - - + +
95F TYR* 3.8 31.6 - - + -
96F VAL* 3.7 16.2 - - + +
99F THR* 5.3 1.6 + - - -
148F LEU* 4.1 13.6 - - + +
149F VAL* 5.4 0.2 - - + -
154F SER* 3.0 11.3 + - - +
155F LEU* 1.3 80.2 - - - +
157F ASP* 1.3 61.5 + - - +
159F ILE* 3.5 1.4 + - - +
160F LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 3.6 8.9 - - - +
148F LEU* 2.8 29.8 + - - +
152F GLN 3.5 6.1 - - - +
153F LEU* 3.3 23.1 - - + -
154F SER* 2.9 33.1 + - - +
156F ALA* 1.3 76.9 - - - +
158F VAL* 1.3 59.8 + - - +
160F LEU* 3.9 0.3 - - - +
161F LEU* 2.8 31.6 + - - +
184F TYR* 2.6 32.7 + - - +
188F LEU* 3.9 9.0 - - + +
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Residues in contact with VAL 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TRP* 3.5 50.0 - - + +
22F VAL* 4.1 16.4 - - + +
25F ALA* 4.0 20.4 - - + -
81F LEU* 5.2 5.6 - - + -
153F LEU* 4.6 13.5 - - + -
154F SER 3.3 13.9 + - - +
155F LEU* 3.2 9.9 + - - +
157F ASP* 1.3 78.5 - - - +
159F ILE* 1.3 53.3 + - + +
161F LEU* 3.5 7.1 - - + +
162F GLN* 2.7 33.3 + - - +
194F ILE* 5.5 3.1 - - + -
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Residues in contact with ILE 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F SER* 3.8 27.8 - - - +
22F VAL* 4.4 7.6 - - + -
72F LEU* 4.3 9.2 - - + -
96F VAL* 4.5 14.4 - - + +
99F THR* 3.8 21.5 - - + -
100F LEU* 3.9 24.0 - - + -
103F LEU* 4.8 0.4 - - + -
155F LEU* 3.2 38.2 + - + +
156F ALA 4.1 2.7 - - - +
158F VAL* 1.3 78.8 - - + +
160F LEU* 1.3 54.1 + - - +
162F GLN* 3.5 10.0 - - - +
163F THR* 2.6 41.5 + - - +
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F THR* 4.1 18.1 - - + +
102F LEU* 6.0 1.6 - - + -
133F PHE* 4.6 8.1 - - + -
136F PHE* 3.8 50.3 - - + -
148F LEU* 3.8 18.6 - - + -
156F ALA 3.0 17.9 + - - +
157F ASP 3.9 2.9 - - - +
159F ILE* 1.3 75.6 - - - +
161F LEU* 1.3 66.1 + - - +
163F THR* 3.1 3.9 + - + -
164F ILE* 2.8 49.5 + - + +
181F LEU* 4.6 4.0 - - + -
184F TYR* 4.0 16.6 - - + +
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TRP* 3.4 28.7 - - + -
157F ASP 2.8 19.4 + - - +
158F VAL* 3.5 5.4 - - - +
160F LEU* 1.3 77.9 - - - +
162F GLN* 1.3 64.8 + - - +
164F ILE* 3.7 6.5 - - + +
165F LEU* 3.0 47.0 + - + +
184F TYR* 5.2 0.2 - - - -
185F THR* 4.0 23.3 - - + +
188F LEU* 4.0 23.9 - - + +
189F SER* 4.0 16.2 - - - +
194F ILE* 3.9 24.0 - - + -
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Residues in contact with GLN 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLU* 3.8 22.0 - - - +
18F SER* 2.7 40.9 + - - +
21F TRP* 3.7 39.5 - - + +
103F LEU* 3.8 21.7 - - + +
158F VAL 2.7 20.3 + - - +
159F ILE* 3.5 12.8 - - - +
161F LEU* 1.3 74.9 - - - +
163F THR* 1.3 63.2 - - - +
165F LEU* 3.6 2.8 + - - +
166F ALA* 3.1 26.6 + - + +
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Residues in contact with THR 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F THR* 3.4 18.5 - - + +
102F LEU* 4.0 31.4 - - + -
103F LEU* 3.8 30.8 - - + +
106F LEU* 4.8 1.8 - - + -
133F PHE* 5.8 0.2 - - + -
159F ILE* 2.6 24.7 + - - +
160F LEU* 3.5 5.4 - - + -
162F GLN* 1.3 77.1 - - - +
164F ILE* 1.3 67.1 + - - +
166F ALA* 3.1 6.0 + - - +
167F LEU* 2.9 35.0 + - + +
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Residues in contact with ILE 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE* 3.8 25.4 - - + -
160F LEU* 2.8 39.6 + - + +
161F LEU* 3.7 6.1 - - - +
163F THR* 1.3 76.7 - - - +
165F LEU* 1.3 68.1 + - + +
167F LEU* 3.0 11.8 + - - +
168F GLU* 2.7 38.8 + - + +
175F LEU* 4.2 25.4 - - + -
181F LEU* 4.4 16.8 - - + -
184F TYR* 4.9 3.4 - - + -
185F THR* 3.9 22.0 - - + +
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TRP* 3.8 31.4 - - + -
161F LEU* 3.0 25.6 + - + +
162F GLN 3.8 3.6 - - - +
164F ILE* 1.3 81.7 - - + +
166F ALA* 1.3 62.7 + - - +
168F GLU* 3.3 21.6 + - - +
169F GLU* 3.1 27.6 + - - +
185F THR* 4.1 23.3 - - + -
189F SER* 5.1 3.1 - - - +
198F LEU* 4.1 19.1 - - + -
204F LYS* 5.6 2.2 - - - -
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ARG* 4.9 7.4 - - - +
103F LEU* 5.0 5.4 - - + -
106F LEU* 4.1 22.9 - - + +
162F GLN* 3.1 16.8 + - + +
163F THR* 3.4 11.4 - - - +
165F LEU* 1.3 73.9 - - - +
167F LEU* 1.3 67.1 + - - +
169F GLU* 3.2 31.4 + - - +
170F LYS* 3.7 9.2 + - - +
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.1 13.9 - - + -
106F LEU* 3.9 20.6 - - + -
124F MET* 3.9 34.3 - - + +
128F ALA* 4.3 4.5 - - + -
133F PHE* 3.8 27.1 - - + -
163F THR* 2.9 31.5 + - + +
164F ILE* 3.3 6.7 - - - +
166F ALA* 1.3 76.8 - - - +
168F GLU* 1.3 52.8 + - - +
170F LYS* 2.6 27.1 + - - +
171F ILE* 2.7 21.8 + - + +
174F ILE* 4.3 20.4 - - + -
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Residues in contact with GLU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ILE* 2.7 28.5 + - + +
165F LEU* 3.7 24.6 - - - +
166F ALA 3.2 0.2 - - - -
167F LEU* 1.3 78.6 - - - +
169F GLU* 1.3 62.1 + - - +
170F LYS 3.2 0.3 + - - -
171F ILE 3.5 9.9 - - - +
172F PRO* 3.3 36.5 - - + +
174F ILE* 3.7 16.2 - - + -
175F LEU* 3.8 26.9 - - - +
185F THR* 5.2 2.6 - - - +
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Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ARG* 2.8 45.3 + - - -
165F LEU* 3.1 21.9 + - - +
166F ALA* 3.4 14.4 - - - +
167F LEU 2.9 1.0 - - - -
168F GLU* 1.3 81.4 - - - +
170F LYS* 1.3 64.7 + - + +
172F PRO* 4.8 3.3 - - - +
204F LYS* 4.6 3.6 + - - -
207F PRO* 3.9 16.3 - - + +
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Residues in contact with LYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 4.2 24.4 + - + -
109F HIS* 2.7 36.9 + - + +
110F PRO* 5.5 1.8 - - - +
121F VAL* 4.4 25.7 - - + +
124F MET* 4.5 7.0 - - + -
166F ALA 4.0 10.8 - - - +
167F LEU* 2.6 12.7 + - - +
169F GLU* 1.3 80.4 - - + +
171F ILE* 1.3 70.4 + - + +
172F PRO* 3.3 9.4 - - - +
208F PRO* 6.3 0.6 - - - +
119G LYS* 5.5 4.3 - - - +
122G VAL* 6.0 0.5 - - - +
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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
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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