Contacts of the helix formed by residues 155 - 170 (chain B) in PDB entry 1GUM
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.5 37.7 - - + -
72B LEU* 4.2 30.3 - - + +
73B HIS* 4.4 15.7 - - + -
76B ALA* 4.2 18.6 - - + -
81B LEU* 2.7 19.2 + - + +
82B PHE* 4.7 7.9 - - + -
92B ILE* 4.1 6.5 - - + -
96B VAL* 4.1 20.6 - - + -
154B SER* 1.3 74.9 - - - +
156B ALA* 1.4 64.2 + - - +
158B VAL* 3.1 6.6 + - - +
159B ILE* 3.1 34.7 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.7 10.3 - - + +
95B TYR* 3.7 34.9 - - + +
96B VAL* 3.5 17.2 - - + +
99B THR* 5.3 1.9 + - - -
148B LEU* 4.0 14.4 - - + +
149B VAL* 5.7 0.4 - - + -
154B SER* 3.1 10.1 + - - +
155B LEU* 1.4 78.3 - - - +
157B ASP* 1.3 57.2 + - - +
159B ILE* 3.5 1.6 + - - +
160B LEU* 3.0 31.9 + - - +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 3.5 7.9 - - - +
148B LEU* 2.8 28.4 + - - +
152B GLN 3.5 5.4 - - - +
153B LEU* 3.2 24.4 - - + -
154B SER* 2.8 35.1 + - - +
156B ALA* 1.3 75.7 - - - +
158B VAL* 1.3 65.2 + - - +
160B LEU* 3.8 0.9 - - - +
161B LEU* 2.9 25.3 + - - +
184B TYR* 2.5 34.3 + - - +
188B LEU* 4.1 7.1 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.8 49.0 - - + +
22B VAL* 4.2 14.6 - - + -
25B ALA* 4.3 17.9 - - + -
81B LEU* 5.1 6.1 - - + -
153B LEU* 4.5 14.6 - - + -
154B SER 3.3 16.8 - - - +
155B LEU* 3.1 8.2 + - - +
157B ASP* 1.3 78.7 - - - +
159B ILE* 1.3 59.2 + - + +
161B LEU* 3.6 5.8 - - - +
162B GLN* 2.9 27.5 + - - +
194B ILE* 5.7 4.9 - - + -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 3.7 29.2 - - - -
22B VAL* 4.7 13.0 - - + -
72B LEU* 4.5 11.7 - - + -
96B VAL* 4.2 19.3 - - + -
99B THR* 4.0 21.3 - - + -
100B LEU* 4.0 24.2 - - + -
155B LEU* 3.1 21.2 + - + +
156B ALA* 4.0 3.1 - - - +
158B VAL* 1.3 78.5 - - + +
160B LEU* 1.3 63.4 + - - +
162B GLN* 3.2 9.2 + - - +
163B THR* 2.8 34.7 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 4.1 17.4 - - + +
102B LEU* 6.1 1.3 - - + -
133B PHE* 4.6 7.6 - - + -
136B PHE* 3.8 49.8 - - + -
148B LEU* 3.9 13.9 - - + -
156B ALA 3.0 19.7 + - - +
157B ASP 3.8 3.1 - - - +
159B ILE* 1.3 78.7 - - - +
161B LEU* 1.3 64.1 + - - +
163B THR* 3.5 2.4 - - + -
164B ILE* 2.8 47.5 + - + +
181B LEU* 4.3 6.7 - - + -
184B TYR* 3.9 22.0 - - + +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.5 24.2 - - + -
157B ASP 2.9 18.4 + - - +
158B VAL* 3.6 6.3 - - - +
160B LEU* 1.3 78.4 - - - +
162B GLN* 1.3 64.2 + - - +
164B ILE* 3.2 6.3 + - + +
165B LEU* 2.9 52.0 + - + +
184B TYR* 5.2 1.3 - - + -
185B THR* 3.9 30.7 - - + +
188B LEU* 4.0 26.5 - - + -
189B SER* 4.0 9.4 - - - +
194B ILE* 4.0 21.1 - - + -
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Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 3.6 25.8 - - - +
18B SER* 2.8 39.3 + - - +
21B TRP* 3.8 40.9 + - + +
103B LEU* 3.7 21.8 - - + +
158B VAL 2.9 17.5 + - - +
159B ILE* 3.3 13.1 - - - +
161B LEU* 1.3 77.6 - - - +
163B THR* 1.3 66.9 - - - +
165B LEU* 3.5 3.1 + - - +
166B ALA* 3.1 22.2 + - + +
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 3.4 19.3 - - + +
102B LEU* 4.0 21.8 - - + -
103B LEU* 3.7 34.0 - - + +
106B LEU* 4.6 0.9 - - + -
133B PHE* 5.9 0.2 - - + -
159B ILE* 2.8 20.3 + - - +
160B LEU* 3.5 4.9 - - + -
162B GLN* 1.3 77.0 - - - +
164B ILE* 1.3 62.7 + - + +
166B ALA* 3.1 6.9 + - - +
167B LEU* 2.7 47.5 + - + +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.9 25.1 - - + -
160B LEU* 2.8 43.6 + - + +
161B LEU* 3.6 5.8 - - - +
163B THR* 1.3 76.7 - - - +
165B LEU* 1.3 68.3 + - + +
167B LEU* 3.1 10.3 + - - +
168B GLU* 2.8 37.4 + - + +
174B ILE* 4.8 0.6 - - + +
175B LEU* 3.9 27.1 - - + -
181B LEU* 4.3 17.5 - - + -
184B TYR* 5.0 3.1 - - + -
185B THR* 3.8 20.9 - - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.8 25.1 - - + -
161B LEU* 2.9 31.1 + - + +
162B GLN 3.8 3.6 - - - +
164B ILE* 1.3 79.0 - - + +
166B ALA* 1.3 59.1 + - - +
168B GLU* 3.0 22.5 + - - +
169B GLU* 2.8 32.5 + - + +
185B THR* 4.1 24.7 - - + -
189B SER* 5.2 2.2 - - - +
198B LEU* 4.3 17.3 - - + -
204B LYS* 5.8 2.5 - - - -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 5.2 5.8 - - - +
103B LEU* 4.8 4.7 - - + -
106B LEU* 3.5 23.7 - - + +
162B GLN* 3.1 14.1 + - + +
163B THR* 3.1 12.3 - - - +
165B LEU* 1.3 78.5 - - - +
167B LEU* 1.3 66.4 + - - +
169B GLU* 3.1 32.8 + - - +
170B LYS* 3.6 9.7 + - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.9 15.9 - - + -
106B LEU* 3.8 13.5 - - + -
124B MET* 3.8 42.0 - - + +
128B ALA* 4.4 4.7 - - + -
133B PHE* 3.9 26.0 - - + -
163B THR* 2.7 34.0 + - + +
164B ILE* 3.4 4.3 - - - +
166B ALA* 1.3 79.5 - - - +
168B GLU* 1.3 51.6 + - - +
170B LYS* 2.7 8.9 + - - +
171B ILE* 2.7 43.5 + - + +
174B ILE* 4.5 11.9 - - + -
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 2.8 30.8 + - + +
165B LEU* 3.0 21.9 + - - +
167B LEU* 1.3 73.0 - - - +
169B GLU* 1.3 67.1 + - - +
170B LYS 3.0 0.2 - - - -
171B ILE 3.5 11.2 - - - +
172B PRO* 3.2 36.6 - - + +
174B ILE* 3.8 11.9 - - + -
175B LEU* 3.8 27.3 - - - +
185B THR* 5.5 2.4 - - - +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.0 43.0 + - - -
165B LEU* 2.8 21.0 + - + +
166B ALA* 3.4 16.0 + - - +
167B LEU 3.0 0.8 - - - -
168B GLU* 1.3 81.5 - - - +
170B LYS* 1.3 69.5 + - + +
172B PRO* 4.9 3.3 - - - +
204B LYS* 4.5 3.5 + - - -
207B PRO* 3.4 19.5 - - + +
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.2 20.9 + - + +
109B HIS* 2.7 46.1 + - + +
110B PRO* 5.2 3.2 - - - +
121B VAL* 4.7 15.9 - - + +
124B MET* 4.6 9.9 - - + -
166B ALA 4.1 9.6 - - - +
167B LEU 2.7 8.1 + - - +
169B GLU* 1.3 90.4 - - + +
171B ILE* 1.3 67.8 + - + +
172B PRO* 3.2 9.8 - - - +
207B PRO* 6.0 4.7 - - - -
208B PRO* 6.1 3.7 - - - +
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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