Contacts of the helix formed by residues 154 - 174 (chain A) in PDB entry 1CG4
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 LYS 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU 4.0 14.4 + - - +
152A PHE 5.6 0.2 - - - -
153A ASP* 1.3 72.7 + - - +
155A GLU* 1.3 58.7 + - + +
157A PHE* 3.3 8.7 - - - +
158A ALA* 2.9 27.9 + - - +
187A LEU* 5.0 0.3 - - - +
191A MET* 3.2 36.6 - - + +
194A ALA* 3.8 22.1 - - - +
195A ASP* 3.1 29.5 + - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP* 3.3 7.0 + - - +
154A LYS* 1.3 73.6 - - + +
156A THR* 1.3 65.1 + - - +
158A ALA* 3.2 9.2 + - - +
159A GLU* 3.0 28.7 + - + +
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 5.6 0.7 - - - +
153A ASP* 2.9 34.2 + - + -
155A GLU* 1.3 76.8 - - - +
157A PHE* 1.3 58.0 + - - +
159A GLU* 3.0 21.9 + - - +
160A LYS* 2.9 61.3 + - + +
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.7 22.9 - - + -
107A LEU* 4.5 8.7 - - + -
146A LEU* 3.8 21.5 - - + -
150A ASP* 3.6 24.0 - - + +
151A LEU* 3.5 25.1 - - + -
153A ASP 2.9 18.5 + - - +
154A LYS* 3.3 10.5 - - - +
155A GLU 3.1 0.2 - - - -
156A THR* 1.3 77.2 - - - +
158A ALA* 1.3 53.4 + - - +
160A LYS* 3.4 6.6 + - - +
161A LEU* 2.7 59.9 + - + +
187A LEU* 3.8 5.4 - - + -
190A THR* 3.7 16.4 - - + -
191A MET* 3.3 26.2 - - + -
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LYS 2.9 12.5 + - - +
155A GLU* 3.4 11.7 - - - +
157A PHE* 1.3 77.1 - - - +
159A GLU* 1.3 57.8 + - + +
161A LEU* 4.4 1.1 - - - -
162A LYS* 2.9 21.1 + - - +
183A TYR* 2.6 30.0 + - - +
187A LEU* 3.5 22.9 - - + -
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 3.0 17.2 + - + +
156A THR* 3.0 24.8 + - + +
158A ALA* 1.3 80.0 - - + +
160A LYS* 1.3 64.4 + - + +
162A LYS* 3.2 4.7 + - - +
163A GLU* 3.1 29.5 + - - +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.7 19.7 - - + -
150A ASP* 2.7 34.7 + - - +
156A THR* 2.9 47.4 + - + +
157A PHE* 3.8 4.9 - - - +
159A GLU* 1.3 72.6 - - + +
161A LEU* 1.3 59.0 + - - +
163A GLU* 3.2 14.7 + - - +
164A VAL* 2.9 31.3 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.6 28.9 - - + -
109A TYR* 4.0 6.7 - - - +
146A LEU* 4.6 5.3 - - + +
157A PHE* 2.7 35.0 + - + +
158A ALA 4.0 0.4 - - - +
160A LYS* 1.3 69.7 - - - +
162A LYS* 1.3 62.2 + - - +
164A VAL* 3.6 4.7 - - + -
165A MET* 2.8 59.7 + - + +
183A TYR* 3.6 13.2 - - + -
186A VAL* 3.9 5.8 - - + -
187A LEU* 3.5 50.3 - - + +
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA 2.9 20.9 + - - +
159A GLU* 3.2 6.5 + - - +
161A LEU* 1.3 74.5 - - - +
163A GLU* 1.3 53.2 + - + +
165A MET* 3.8 1.1 - - - +
166A GLU* 2.3 82.8 + - - +
183A TYR* 3.0 44.7 - - + +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 3.1 21.5 + - - +
160A LYS* 3.3 14.7 + - - +
162A LYS* 1.3 75.7 - - + +
164A VAL* 1.3 67.6 + - - +
166A GLU* 3.1 18.5 - - - +
167A TYR* 3.0 23.1 + - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 3.5 21.8 - - - +
139A ASP* 3.7 11.0 - - - +
144A ARG* 3.7 30.3 - - + +
146A LEU* 3.6 13.0 - - + -
160A LYS 2.9 14.6 + - - +
161A LEU* 3.2 14.4 - - - +
163A GLU* 1.3 77.1 - - - +
165A MET* 1.3 63.5 + - + +
167A TYR* 3.4 6.8 - - - +
168A HIS* 2.9 58.0 + - + +
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Residues in contact with MET 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 3.7 26.7 - - + -
161A LEU* 2.8 54.6 + - + +
162A LYS 3.9 2.2 - - - +
164A VAL* 1.3 75.8 - - - +
166A GLU* 1.3 57.5 + - - +
168A HIS* 3.1 4.6 + - - +
169A ASN* 2.6 45.8 + - - +
181A VAL* 3.3 31.6 - - + +
183A TYR* 3.6 30.5 - - + -
186A VAL* 3.7 22.9 - - + -
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LYS* 2.3 71.0 + - - +
163A GLU* 3.1 24.5 - - - +
165A MET* 1.3 74.3 - - - +
167A TYR* 1.3 63.0 + - - +
169A ASN* 3.1 9.5 + - - +
170A PHE* 2.8 26.1 + - - +
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 3.4 48.7 + - - -
163A GLU 3.0 12.8 + - - +
164A VAL* 3.4 10.3 - - - +
166A GLU* 1.3 79.2 - - - +
168A HIS* 1.3 86.5 + + - +
170A PHE* 3.5 15.7 + - - +
171A GLN* 3.6 17.3 + - + +
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 3.4 36.0 - + + -
113A LEU* 3.5 24.8 - - + +
117A ARG* 5.8 1.9 + - - -
139A ASP* 3.0 41.8 + - - -
144A ARG* 4.0 2.1 + - - -
164A VAL* 2.9 31.8 + - + +
165A MET* 3.9 2.7 - - - +
167A TYR* 1.3 94.9 - + - +
169A ASN* 1.3 66.8 + - - +
171A GLN* 3.1 24.1 + - - +
172A LEU* 3.0 26.7 + - + +
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 5.9 1.0 - - - +
165A MET* 2.6 37.6 + - - +
166A GLU* 3.4 8.4 - - - +
168A HIS* 1.3 71.8 - - - +
170A PHE* 1.3 64.8 + - - +
172A LEU* 3.0 17.1 + - - +
173A VAL* 3.1 20.2 + - + +
180A ALA* 3.3 14.1 - - + +
181A VAL* 2.7 48.2 + - - +
183A TYR* 4.8 5.3 - - - +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU 2.8 12.6 + - - +
167A TYR* 3.6 12.1 - - - +
168A HIS 3.2 0.2 - - - -
169A ASN* 1.3 74.9 - - - +
171A GLN* 1.3 62.4 + - + +
173A VAL* 4.7 2.9 - - - -
174A ASN* 3.0 60.8 + - + +
175A TYR* 5.8 1.3 - - + -
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.8 8.2 - - - +
117A ARG* 2.8 33.4 + - - +
167A TYR* 3.6 16.3 + - + +
168A HIS* 3.1 32.6 + - - +
170A PHE* 1.3 86.2 - - + +
172A LEU* 1.3 61.0 + - - +
175A TYR* 3.1 18.1 + - + +
176A TYR* 3.1 47.1 + - + -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 4.8 9.2 - - + +
112A ALA* 3.7 31.9 - - + -
113A LEU* 3.9 23.1 - - + -
116A ALA* 4.2 14.8 - - + -
168A HIS 3.0 19.0 + - - +
169A ASN* 3.0 15.4 + - - +
171A GLN* 1.3 75.3 - - - +
173A VAL* 1.3 54.2 + - + +
176A TYR* 3.3 13.9 - - + +
177A LYS 3.0 8.5 + - - -
178A ALA* 2.5 42.1 + - + +
179A GLU 4.1 16.4 - - - +
181A VAL* 4.1 14.1 - - + -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN 3.1 13.4 + - - +
170A PHE* 3.8 5.8 - - - +
172A LEU* 1.3 75.5 - - - +
174A ASN* 1.3 88.1 + - - +
177A LYS* 2.9 25.3 - - - +
178A ALA 3.1 17.5 - - - +
179A GLU* 4.8 0.2 - - - -
180A ALA* 3.7 30.7 - - + +
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.0 59.3 + - + +
173A VAL* 1.3 96.1 - - - +
175A TYR* 1.3 60.2 + - - +
177A LYS* 3.0 24.8 + - - +
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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