Contacts of the helix formed by residues 153 - 168 (chain A) in PDB entry 4OG6
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 ASP 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS 3.5 22.4 - - - +
136A ASP* 5.4 1.1 - - - -
137A ARG 4.8 5.1 - - - +
140A ILE* 3.0 20.1 + - + +
141A GLN* 3.6 24.5 + - - +
152A LEU* 1.3 75.1 - - - +
154A SER* 1.3 65.4 + - - +
155A SER* 3.9 7.7 + - - -
156A GLY* 2.9 29.5 + - - -
157A VAL* 3.1 20.1 + - - +
198A TRP* 3.8 2.5 - - - -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS 4.7 1.0 + - - -
153A ASP* 1.3 76.9 - - - +
155A SER* 1.3 63.4 + - - +
157A VAL 3.2 5.5 + - - -
158A ALA 3.6 0.3 + - - -
181A HIS* 4.6 3.8 + - - -
182A ALA 5.8 0.2 + - - -
197A THR* 2.8 30.1 + - - +
198A TRP* 2.6 57.1 + - - -
199A HIS* 4.5 3.0 - - - -
200A GLY 5.7 1.3 - - - -
602A 2S9 5.6 2.7 - - - -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 3.4 7.5 + - - -
154A SER* 1.3 80.7 - - - +
156A GLY* 1.3 57.9 + - - +
158A ALA* 3.1 4.9 + - - +
159A PHE* 3.0 27.2 + - - +
175A LEU* 5.2 0.3 - - - +
182A ALA* 3.9 17.2 - - - +
238A PHE* 3.7 25.6 - - - -
602A 2S9 3.6 42.5 - - - +
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Residues in contact with GLY 156 (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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141A GLN* 3.8 19.8 - - - +
152A LEU* 3.6 12.7 - - - +
153A ASP* 2.9 23.7 + - - -
155A SER* 1.3 74.8 + - - +
157A VAL* 1.3 58.9 + - - +
159A PHE* 3.4 6.4 + - - +
160A ALA* 2.9 29.6 + - - +
238A PHE* 5.7 1.3 - - - -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 5.3 1.1 - - - +
125A ILE* 4.1 15.3 - - + -
126A TRP* 5.0 10.5 - - + +
129A LEU* 4.0 12.3 - - + -
152A LEU* 3.8 22.7 - - + -
153A ASP 3.1 13.6 + - - +
154A SER 3.2 0.4 + - - +
156A GLY* 1.3 77.7 - - - +
158A ALA* 1.3 61.9 + - - +
160A ALA* 3.2 2.6 + - - +
161A VAL* 2.9 26.7 + - + +
196A VAL 3.8 19.3 - - - +
197A THR* 3.4 17.9 - - - +
198A TRP* 3.6 22.7 - - + -
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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
----------------------------------------------------------
154A SER 3.6 2.6 + - - -
155A SER 3.1 9.2 + - - +
157A VAL* 1.3 77.9 - - - +
159A PHE* 1.3 63.3 + - - +
161A VAL* 3.2 3.5 + - - +
162A VAL* 3.1 26.3 + - - +
175A LEU* 3.8 10.5 - - + -
182A ALA* 3.7 31.0 - - + +
183A TRP* 4.3 1.3 - - - +
184A VAL* 4.5 0.7 - - - +
196A VAL* 3.7 27.1 - - + -
197A THR* 4.2 4.4 - - + -
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.1 25.8 - - + -
38A SER* 3.6 26.9 - - - -
141A GLN 5.0 8.3 - - - +
143A LEU* 4.5 12.8 - - + -
155A SER 3.0 12.7 + - - +
156A GLY* 3.8 10.5 - - - +
158A ALA* 1.3 75.8 - - - +
160A ALA* 1.3 62.0 + - - +
162A VAL* 3.1 7.8 + - + +
163A GLY* 2.9 24.6 + - - -
175A LEU* 4.1 14.4 - - + +
235A GLU* 3.8 22.7 - - + -
238A PHE* 3.9 29.6 - + + -
239A MET* 3.6 33.9 - - + -
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Residues in contact with ALA 160 (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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93A PHE* 4.1 3.7 - - + -
125A ILE* 4.1 16.6 - - + +
143A LEU* 3.6 29.6 - - + -
146A PHE* 5.3 0.7 - - + -
152A LEU* 3.7 15.9 - - + -
156A GLY 2.9 18.3 + - - +
157A VAL 3.2 5.1 + - - +
159A PHE* 1.3 72.4 - - - +
161A VAL* 1.3 61.1 + - - +
163A GLY* 3.3 1.6 + - - +
164A ALA* 2.9 31.5 + - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.7 5.8 - - + +
121A VAL* 4.0 20.2 - - + -
122A SER* 3.8 27.1 - - - +
125A ILE* 4.1 12.8 - - + -
157A VAL* 2.9 21.8 + - + +
158A ALA 3.2 8.0 + - - +
160A ALA* 1.3 77.4 - - - +
162A VAL* 1.3 57.6 + - - +
164A ALA* 3.4 1.7 + - - +
165A CYS* 2.9 37.0 + - - -
173A VAL* 5.2 0.2 - - + -
184A VAL* 4.3 8.7 - - + -
196A VAL* 4.2 31.2 - - + -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.0 7.2 - - + -
158A ALA 3.1 15.8 + - - +
159A PHE* 3.6 9.4 - - + +
161A VAL* 1.3 75.1 - - - +
163A GLY* 1.3 57.6 + - - +
165A CYS* 3.2 7.1 + - - +
166A GLN* 2.9 27.7 + - - +
173A VAL* 3.8 9.9 - - + +
174A HIS* 3.9 2.2 - - - -
175A LEU* 3.6 27.6 - - + +
184A VAL* 3.7 20.0 - - + -
232A ARG* 3.5 26.1 + - - +
235A GLU* 3.8 17.9 - - + +
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Residues in contact with GLY 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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34A LEU* 4.4 18.5 - - - +
35A VAL* 3.6 22.6 - - - +
93A PHE* 4.3 0.7 - - - -
143A LEU* 5.2 3.8 - - - -
159A PHE* 2.9 15.3 + - - -
160A ALA* 3.3 3.8 + - - -
162A VAL* 1.3 75.0 - - - +
164A ALA* 1.3 62.0 + - - +
166A GLN* 3.3 2.9 + - - +
167A ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 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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93A PHE* 3.9 13.1 - - + -
97A ILE* 3.9 28.8 - - + +
121A VAL* 3.7 19.3 - - + -
125A ILE* 4.6 1.8 - - + -
160A ALA 2.9 16.8 + - - +
161A VAL* 3.6 4.3 - - - +
163A GLY* 1.3 77.9 - - - +
165A CYS* 1.3 56.8 + - - +
167A ALA* 3.3 4.8 + - - +
168A LEU* 3.0 33.7 + - - +
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Residues in contact with CYS 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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118A VAL* 5.3 6.1 - - - -
121A VAL* 4.0 22.2 - - - -
161A VAL* 2.9 25.3 + - - +
162A VAL 3.6 4.7 - - - +
164A ALA* 1.3 73.8 - - - +
166A GLN* 1.3 64.8 + - - +
168A LEU* 3.1 8.8 + - - +
169A GLY 3.2 0.2 + - - -
170A LEU* 2.9 49.0 + - + +
173A VAL* 3.8 38.6 - - + +
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Residues in contact with GLN 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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31A GLU* 3.0 34.2 + - - +
32A PRO 2.9 23.4 + - - -
33A ASP* 3.7 7.7 - - - +
34A LEU* 2.9 35.5 + - + +
35A VAL* 4.3 1.7 + - - +
162A VAL 2.9 15.1 + - - +
163A GLY* 3.7 5.5 - - - +
165A CYS* 1.3 74.6 - - - +
167A ALA* 1.3 65.4 + - - +
169A GLY* 2.9 15.0 + - - -
170A LEU 4.5 2.5 - - - +
171A ARG* 6.0 0.2 - - - +
232A ARG* 3.6 29.2 - - - +
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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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35A VAL* 4.6 9.8 - - + +
90A TYR* 6.0 1.3 - - - +
93A PHE* 4.8 3.1 - - + -
94A THR* 4.5 15.0 - - + -
97A ILE* 5.3 4.3 - - + -
98A ARG* 2.8 35.8 + - - +
163A GLY 3.0 14.1 + - - +
164A ALA* 3.4 12.8 - - - +
165A CYS 3.3 0.4 - - - -
166A GLN* 1.3 77.1 - - - +
168A LEU* 1.3 61.2 + - + +
169A GLY 3.4 0.9 + - - -
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Residues in contact with LEU 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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97A ILE* 3.6 25.6 - - + -
98A ARG* 4.2 21.3 - - + +
101A VAL* 3.9 31.6 - - + +
103A LEU* 3.5 39.6 - - + +
121A VAL* 4.0 16.4 - - + -
164A ALA 3.0 19.1 + - - +
165A CYS* 3.1 10.4 + - - +
167A ALA* 1.3 74.2 - - - +
169A GLY* 1.3 58.0 + - - +
170A LEU* 3.5 15.9 + - + +
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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
------------------------------------------------------------
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