Contacts of the helix formed by residues 163 - 177 (chain A) in PDB entry 3ECP
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 GLY 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLU* 5.9 2.2 - - - -
160A LYS* 3.2 11.3 + - - +
161A GLU 3.2 1.8 - - - -
162A SER* 1.3 76.7 + - - +
164A LYS* 1.3 57.7 + - - +
165A TRP 3.2 0.9 - - - -
166A LEU* 3.1 16.2 + - - +
167A ALA* 2.9 29.6 + - - +
503A GOL 4.1 4.7 - - - -
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Residues in contact with LYS 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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98A THR* 2.7 37.1 + - - +
127A HIS* 3.6 23.6 - - + +
146A GLU* 4.1 9.8 - - - +
148A TRP* 3.9 15.0 - - + -
161A GLU* 3.0 20.3 + - + +
162A SER* 3.0 2.7 - - - +
163A GLY* 1.3 78.6 - - - +
165A TRP* 1.3 88.3 - - + +
167A ALA* 3.8 1.9 - - - +
168A ALA* 3.0 30.0 + - - +
190A GLU* 3.1 23.5 + - - -
503A GOL 3.0 21.8 + - - +
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Residues in contact with TRP 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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96A GLU* 3.4 40.9 - - + +
97A ASP* 4.6 5.6 - - - -
127A HIS* 3.7 13.5 - + - -
162A SER* 3.0 27.7 - - - +
163A GLY 3.2 0.4 - - - -
164A LYS* 1.3 104.7 - - + +
166A LEU* 1.3 61.2 + - + +
168A ALA* 3.7 3.3 + - - +
169A ALA* 3.3 14.6 + - - +
187A CYS* 3.5 27.8 - - + -
188A ASP* 3.8 20.4 - - - -
190A GLU* 3.5 36.6 + - + +
191A ALA* 3.5 21.8 - - + -
193A ILE* 3.9 14.3 - - + +
196A TYR* 3.3 36.4 - + + -
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Residues in contact with LEU 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 SER 5.0 2.7 - - - +
163A GLY* 3.1 17.7 + - - +
165A TRP* 1.3 77.4 - - + +
167A ALA* 1.3 64.8 + - - +
168A ALA 3.1 1.8 - - - -
169A ALA* 2.9 9.0 + - - +
170A ALA* 2.9 24.0 + - - +
173A ARG* 5.1 0.5 + - - -
193A ILE* 5.7 2.9 - - + -
195A ALA* 4.0 14.1 - - + +
196A TYR* 3.8 33.7 - - + +
199A ASP* 3.5 37.5 - - + +
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Residues in contact with ALA 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 HIS* 4.6 3.6 - - + +
146A GLU* 3.7 26.9 - - - +
163A GLY 2.9 16.7 + - - +
164A LYS 3.8 1.3 - - - +
166A LEU* 1.3 75.1 - - - +
168A ALA* 1.3 61.3 + - - +
170A ALA* 3.4 8.7 + - - +
171A THR* 3.1 26.3 + - - -
503A GOL 5.3 2.2 - - - -
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Residues in contact with ALA 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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96A GLU* 3.2 35.9 - - - +
127A HIS* 4.2 1.6 - - + -
129A VAL* 4.1 2.9 - - + -
144A HIS* 3.5 32.0 + - + +
164A LYS 3.0 12.8 + - - +
165A TRP 3.8 0.7 - - - +
167A ALA* 1.3 73.1 - - - +
169A ALA* 1.3 62.7 + - - +
171A THR* 3.2 2.8 + - - -
172A SER* 2.7 32.6 + - - -
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Residues in contact with ALA 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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96A GLU* 5.2 1.3 + - - -
165A TRP 3.3 11.1 + - - +
166A LEU* 2.9 9.7 + - - +
168A ALA* 1.3 77.3 - - - +
170A ALA* 1.3 65.1 + - - +
172A SER* 3.0 7.5 + - - -
173A ARG* 2.9 49.0 + - - +
180A MET* 5.0 1.9 - - - +
196A TYR* 4.7 2.0 - - + +
199A ASP* 3.9 8.5 - - - +
200A LYS* 4.6 14.4 - - + +
205A GLU* 4.2 7.8 - - - +
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Residues in contact with ALA 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 LEU 2.9 10.9 + - - +
167A ALA* 3.5 13.0 - - - +
169A ALA* 1.3 77.5 - - - +
171A THR* 1.3 59.8 + - - +
173A ARG* 3.4 24.4 - - - +
174A LEU* 3.4 23.7 + - - +
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Residues in contact with THR 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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144A HIS* 3.5 33.3 - - + +
167A ALA 3.1 16.6 + - - -
168A ALA 3.2 2.9 + - - -
169A ALA 3.2 0.2 - - - -
170A ALA* 1.3 74.2 - - - +
172A SER* 1.3 61.7 + - - +
174A LEU* 3.4 7.9 + - + +
175A ARG* 2.8 68.1 + - - +
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Residues in contact with SER 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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129A VAL* 4.5 13.7 - - - +
143A LEU* 3.8 33.3 - - - +
144A HIS* 4.9 1.6 - - - +
168A ALA 2.7 22.1 + - - -
169A ALA* 3.6 5.4 - - - -
171A THR* 1.3 76.1 - - - +
173A ARG* 1.3 54.5 + - - +
175A ARG 3.1 0.9 + - - -
176A MET* 2.5 38.5 + - - +
180A MET* 3.8 22.9 - - - -
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Residues in contact with ARG 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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166A LEU 5.1 0.4 + - - -
169A ALA* 2.9 16.1 + - - +
170A ALA* 3.4 39.3 - - - +
172A SER* 1.3 76.6 - - - +
174A LEU* 1.3 58.0 + - + +
177A GLY* 2.6 38.4 + - - +
180A MET* 3.6 17.7 - - + -
199A ASP* 3.0 26.9 + - - -
203A HIS* 3.3 40.0 + - - -
205A GLU* 2.6 46.9 + - - +
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Residues in contact with LEU 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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80A MET* 5.6 0.3 - - - +
170A ALA 3.4 16.5 + - - +
171A THR* 3.6 7.9 - - + +
173A ARG* 1.3 82.4 - - + +
175A ARG* 1.3 75.7 + - + +
177A GLY* 3.8 7.2 + - - -
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Residues in contact with ARG 175 (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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75A ARG 5.4 0.6 - - - -
76A LYS* 3.9 44.4 - - - +
79A ALA* 3.7 13.2 - - - +
80A MET* 4.0 22.7 - - + +
83A VAL* 3.5 22.9 - - + +
143A LEU* 2.8 47.3 + - + -
144A HIS* 5.1 5.1 + - - +
145A GLN 5.8 0.4 - - - +
171A THR* 2.8 43.6 + - - +
172A SER 3.7 1.8 - - - +
174A LEU* 1.3 89.9 - - + +
176A MET* 1.3 61.5 + - - +
177A GLY 3.5 0.3 + - - -
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Residues in contact with MET 176 (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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83A VAL* 4.3 6.0 - - - +
86A ALA* 4.1 7.6 - - + -
92A LEU* 3.9 13.9 - - + -
131A LEU* 3.9 26.7 - - + -
143A LEU* 3.7 26.7 - - + -
172A SER 2.5 23.8 + - - +
175A ARG* 1.3 73.3 - - - +
177A GLY* 1.3 56.8 + - - +
178A SER 3.2 0.9 + - - -
179A MET* 3.0 57.4 + - + +
180A MET* 4.0 24.0 - - - +
183A VAL* 3.2 29.6 - - + -
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Residues in contact with GLY 177 (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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173A ARG* 2.6 23.0 + - - +
174A LEU 4.2 6.5 - - - -
175A ARG 3.3 3.0 - - - -
176A MET* 1.3 70.1 - - - +
178A SER* 1.3 61.1 + - - -
179A MET 3.2 1.1 + - - -
180A MET* 3.4 18.7 + - - +
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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
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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