Contacts of the helix formed by residues 163 - 177 (chain A) in PDB entry 3G26
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 SER 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLN* 3.3 2.9 + - - +
161A SER 4.1 1.2 + - - -
162A GLU* 1.3 78.3 - - - +
164A PHE* 1.3 65.4 + - - +
165A VAL* 3.6 11.3 - - - +
166A ASP* 2.8 35.9 + - - +
167A PHE* 3.1 22.0 + - - +
226A GLN* 5.8 3.4 - - - -
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Residues in contact with PHE 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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158A GLN* 3.2 13.5 - - - +
163A SER* 1.3 73.6 - - - +
165A VAL* 1.3 61.1 + - - +
167A PHE* 3.1 31.0 + + - +
168A ALA* 2.8 34.3 + - + +
193A PHE* 4.1 25.8 - + - -
197A SER* 4.1 5.2 - - - -
201A ILE* 3.5 41.0 - - + +
205A ILE* 4.1 14.6 - - + -
218A ILE* 4.9 0.9 - - + -
219A ILE* 4.1 23.8 - - + -
222A VAL* 3.7 31.9 - - + -
223A LEU* 3.8 9.4 - - + -
226A GLN* 4.8 10.2 - - - +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A SER* 3.6 12.7 - - - +
164A PHE* 1.3 83.3 - - - +
166A ASP* 1.3 65.8 + - - +
168A ALA* 3.2 4.6 + - + +
169A ASN* 2.9 53.7 + - - +
219A ILE* 4.6 10.8 - - + -
223A LEU* 4.0 36.0 - - + +
226A GLN* 5.5 0.8 + - - -
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Residues in contact with ASP 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 GLU* 3.6 22.7 - - + +
163A SER* 2.8 27.8 + - - +
165A VAL* 1.3 83.2 - - - +
167A PHE* 1.3 59.0 - - - +
169A ASN* 3.3 8.8 + - - +
170A ARG* 3.0 29.5 + - - +
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Residues in contact with PHE 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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156A ILE* 3.9 28.7 - - + -
157A MET 3.7 3.8 - - - -
158A GLN* 3.3 42.4 - - + -
162A GLU* 3.4 14.7 + - - +
163A SER 3.1 12.9 + - - +
164A PHE* 3.5 35.7 - + - +
166A ASP* 1.3 74.7 - - - +
168A ALA* 1.3 61.1 + - - +
170A ARG* 3.2 3.3 + - - +
171A LEU* 2.8 46.9 + - + +
192A CYS 3.6 20.6 - - - -
193A PHE* 3.9 14.4 - + - -
196A LYS* 3.8 12.1 - - + -
197A SER* 4.0 8.5 - - - -
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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
----------------------------------------------------------
164A PHE* 2.8 31.9 + - + +
165A VAL* 3.6 9.6 - - + +
167A PHE* 1.3 74.2 - - - +
169A ASN* 1.3 60.8 + - - +
171A LEU* 3.5 0.9 + - - +
172A ILE* 2.9 36.8 + - - +
193A PHE* 3.7 33.4 - - + -
219A ILE* 4.3 11.9 - - + -
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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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165A VAL* 2.9 39.9 + - - +
166A ASP* 3.7 8.0 - - - +
168A ALA* 1.3 79.9 - - - +
170A ARG* 1.3 57.0 + - - +
172A ILE* 3.9 8.1 - - - +
173A LYS* 3.0 30.5 + - - +
219A ILE* 5.6 2.9 - - - +
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Residues in contact with ARG 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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156A ILE* 3.7 36.3 - - + +
157A MET 3.0 27.9 + - - +
159A GLY 4.7 0.6 - - - +
162A GLU* 2.8 32.7 + - - -
166A ASP 3.0 14.1 + - - +
167A PHE* 3.7 3.7 - - - +
169A ASN* 1.3 74.2 - - - +
171A LEU* 1.3 64.1 + - - +
173A LYS* 3.4 7.0 + - - +
174A ALA* 3.1 24.4 + - - +
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Residues in contact with LEU 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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153A TRP* 3.9 21.5 - - + +
156A ILE* 3.9 21.9 - - + +
167A PHE* 2.8 27.9 + - + +
168A ALA 3.7 1.6 - - - +
170A ARG* 1.3 76.7 - - - +
172A ILE* 1.3 58.0 + - - +
174A ALA* 3.2 4.2 + - - +
175A VAL* 2.9 45.4 + - + +
189A ILE* 3.9 8.5 - - + +
192A CYS* 3.5 39.7 - - + -
193A PHE* 3.5 32.5 - - + -
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Residues in contact with ILE 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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168A ALA 2.9 22.9 + - - +
169A ASN* 4.0 7.0 - - - +
171A LEU* 1.3 76.4 - - - +
173A LYS* 1.3 58.9 + - - +
175A VAL* 3.2 6.7 + - - +
176A GLU* 2.9 51.0 + - + +
189A ILE* 3.8 33.0 - - + -
193A PHE* 3.9 19.3 - - + -
215A PRO* 4.5 6.5 - - + -
219A ILE* 4.1 16.4 - - + -
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Residues in contact with LYS 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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150A ALA* 4.3 7.4 - - + +
169A ASN 3.0 17.7 + - - +
170A ARG* 3.8 7.0 - - - +
172A ILE* 1.3 78.9 - - - +
174A ALA* 1.3 60.7 + - - +
176A GLU* 3.4 7.6 + - + +
177A GLY* 3.1 19.6 + - - -
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Residues in contact with ALA 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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150A ALA* 4.3 9.0 - - - +
151A GLY* 3.4 31.5 - - - +
153A TRP* 3.6 8.1 - - + +
156A ILE* 3.4 32.1 - - + -
170A ARG 3.1 8.1 + - - +
171A LEU 3.2 2.0 + - - +
173A LYS* 1.3 77.6 - - - +
175A VAL* 1.3 62.5 + - - +
177A GLY* 3.3 3.5 + - - -
178A SER* 3.2 20.6 + - - -
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Residues in contact with VAL 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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153A TRP* 3.7 25.1 - - + -
171A LEU* 2.9 30.7 + - + +
172A ILE 3.2 3.8 + - - +
174A ALA* 1.3 75.3 - - - +
176A GLU* 1.3 61.6 + - - +
178A SER* 2.7 27.1 + - - +
180A LEU* 4.3 11.2 - - + -
185A ARG* 3.8 42.3 + - + +
188A VAL* 4.3 8.7 - - + -
189A ILE* 3.9 24.9 - - + -
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Residues in contact with GLU 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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172A ILE* 2.9 37.0 + - + +
173A LYS* 3.7 7.2 - - + +
175A VAL* 1.3 75.4 - - + +
177A GLY* 1.3 59.6 + - - +
178A SER 3.3 3.9 + - - +
185A ARG* 3.3 51.4 + - - +
189A ILE* 4.5 5.9 - - - +
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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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150A ALA* 3.7 28.6 + - - -
173A LYS 3.1 13.5 + - - -
174A ALA 3.3 5.4 + - - -
175A VAL 3.1 0.4 - - - -
176A GLU* 1.3 74.4 - - - +
178A SER* 1.3 63.8 + - - +
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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