Contacts of the helix formed by residues 149 - 163 (chain Z) in PDB entry 3EXG
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 ASN 149 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5Z VAL* 3.7 3.8 - - - +
148Z TRP* 1.3 106.3 - - + +
150Z SER* 1.3 64.4 + - - +
151Z GLU* 2.9 14.8 + - - +
152Z ASP* 2.7 43.7 + - - +
153Z ALA* 3.1 19.8 + - - +
180Z PHE* 3.4 38.1 - - + -
199Z LYS* 5.5 2.6 - - - +
201Z GLU* 3.9 8.5 + - - -
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Residues in contact with SER 150 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Z VAL* 2.9 28.4 + - - -
5Z VAL* 3.3 23.2 + - - +
8Z ALA* 3.2 27.4 - - - +
149Z ASN* 1.3 74.2 - - - +
151Z GLU* 1.3 67.6 + - - +
153Z ALA* 3.2 2.4 + - - +
154Z LYS* 3.1 17.3 + - - +
180Z PHE* 3.5 19.4 - - - -
182Z PHE* 3.7 11.2 - - - -
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Residues in contact with GLU 151 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149Z ASN* 2.9 12.1 + - - +
150Z SER* 1.3 81.0 - - - +
152Z ASP* 1.3 66.0 + - - +
154Z LYS* 3.2 1.2 + - - -
155Z GLY 3.2 16.5 + - - -
180Z PHE* 5.3 1.7 - - + +
181Z GLU 6.0 0.2 - - - +
182Z PHE* 3.5 14.0 - - + -
183Z PRO* 2.9 33.4 - - + +
186Z ALA* 4.2 9.2 - - + -
191Z PHE* 3.6 36.5 - - + -
193Z ILE* 3.8 2.4 - - + +
199Z LYS* 4.1 19.9 + - - -
239Z ARG* 4.5 9.5 + - - -
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Residues in contact with ASP 152 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Z PRO* 3.8 8.5 - - + -
148Z TRP* 2.9 30.7 + - - +
149Z ASN* 2.7 40.3 + - - +
151Z GLU* 1.3 73.0 - - - +
153Z ALA* 1.3 63.9 + - - +
155Z GLY 3.2 0.2 + - - -
156Z LEU* 3.0 28.5 + - + +
193Z ILE* 3.6 9.2 - - - +
199Z LYS* 4.8 0.3 - - - +
201Z GLU* 4.3 1.6 - - - +
237Z ASN* 3.0 20.9 - - - +
239Z ARG* 3.4 30.0 + - - -
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Residues in contact with ALA 153 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Z VAL* 3.6 24.5 - - + +
9Z ILE* 3.5 29.9 - - + +
147Z PRO* 3.6 22.0 - - + -
149Z ASN 3.1 3.3 + - - +
150Z SER 3.2 4.9 + - - +
152Z ASP* 1.3 78.6 - - - +
154Z LYS* 1.3 58.0 + - - +
156Z LEU* 4.1 0.6 - - - +
157Z ILE* 2.9 34.1 + - - +
169Z VAL* 5.9 0.7 - - - +
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Residues in contact with LYS 154 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Z ALA* 3.4 28.4 - - + +
11Z GLN* 2.8 25.9 + - + +
12Z GLY* 4.3 2.0 - - - +
15Z GLU* 2.7 41.7 + - - -
150Z SER 3.1 14.3 + - - +
151Z GLU 3.9 2.7 - - - +
152Z ASP 3.2 0.2 - - - -
153Z ALA* 1.3 76.3 - - - +
155Z GLY* 1.3 64.3 + - - +
157Z ILE* 3.2 11.1 - - - +
158Z LYS* 3.1 35.3 - - + +
182Z PHE* 3.9 9.2 - - + -
186Z ALA 3.0 25.5 + - - +
187Z GLN 3.1 8.1 + - - -
188Z SER 3.4 6.3 + - - -
191Z PHE* 4.2 9.4 - - + -
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Residues in contact with GLY 155 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Z GLU 3.2 10.9 + - - -
154Z LYS* 1.3 77.5 - - - +
156Z LEU* 1.3 58.2 + - - +
158Z LYS* 3.2 2.9 + - - +
159Z SER* 2.9 33.3 + - - -
191Z PHE* 3.8 16.3 - - - -
192Z LEU* 4.5 0.2 - - - -
193Z ILE* 3.6 32.7 + - - -
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Residues in contact with LEU 156 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145Z VAL* 4.2 28.5 - - + +
147Z PRO* 3.6 42.6 - - + -
152Z ASP* 3.0 16.9 + - + +
153Z ALA* 4.1 2.9 - - - +
155Z GLY* 1.3 74.4 - - - +
157Z ILE* 1.3 65.2 + - - +
159Z SER* 3.9 1.1 - - - -
160Z ALA* 3.0 26.2 + - - +
169Z VAL* 4.8 4.4 - - + +
193Z ILE* 3.6 34.3 - - + +
194Z PRO 5.2 0.2 - - - +
195Z ILE* 4.7 10.9 - - + +
239Z ARG* 4.2 29.6 - - + +
240Z THR* 5.0 0.2 - - - +
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Residues in contact with ILE 157 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z ILE* 4.2 18.2 - - + +
12Z GLY* 4.0 22.7 - - - -
13Z MET* 4.6 10.5 - - + -
77Z ILE* 5.6 0.9 - - + -
113Z VAL* 4.9 4.7 - - + -
115Z ARG* 3.5 31.9 - - + -
153Z ALA 2.9 21.4 + - - +
154Z LYS* 3.2 17.7 - - - +
156Z LEU* 1.3 73.1 - - - +
158Z LYS* 1.3 61.2 + - + +
160Z ALA* 3.7 3.3 - - - +
161Z ILE* 3.0 35.4 + - + +
169Z VAL* 3.9 29.7 - - + +
171Z GLU* 4.0 5.6 - - - +
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Residues in contact with LYS 158 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLY* 3.8 13.8 + - - -
15Z GLU* 2.7 42.6 + - - +
16Z GLU* 2.7 40.9 + - + +
154Z LYS* 3.1 30.3 - - + +
155Z GLY 3.2 3.7 + - - +
156Z LEU 3.1 0.6 - - - -
157Z ILE* 1.3 75.6 - - + +
159Z SER* 1.3 60.5 + - - +
160Z ALA 3.0 1.1 - - - -
161Z ILE* 2.8 20.6 + - - +
162Z ARG* 3.0 17.7 + - - +
189Z LYS 3.7 18.6 + - - -
190Z ASP 4.8 0.4 - - - -
191Z PHE 3.3 20.6 - - - +
192Z LEU* 4.0 11.4 - - + -
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Residues in contact with SER 159 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155Z GLY 2.9 15.6 + - - -
156Z LEU 3.9 3.6 - - - -
158Z LYS* 1.3 77.0 - - - +
160Z ALA* 1.3 56.5 + - - +
162Z ARG* 3.9 5.4 - - - +
163Z ASP* 3.0 28.6 + - - +
192Z LEU* 3.6 16.8 - - - +
193Z ILE 2.9 32.8 + - - -
194Z PRO* 4.3 2.4 - - - +
195Z ILE* 4.1 17.3 - - - +
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Residues in contact with ALA 160 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Z VAL* 3.2 14.4 - - + +
156Z LEU 3.0 19.1 + - - +
157Z ILE 3.7 6.5 - - - +
159Z SER* 1.3 74.7 - - - +
161Z ILE* 1.3 62.5 + - - +
163Z ASP* 3.5 6.1 + - - +
167Z VAL* 3.8 30.8 - - + +
169Z VAL* 4.0 13.0 - - + -
195Z ILE* 4.3 8.7 - - + +
1010Z K 2.7 19.6 - - - -
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Residues in contact with ILE 161 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLY 5.0 0.7 - - - +
13Z MET* 4.8 7.2 - - + -
16Z GLU* 3.8 35.9 - - + +
19Z ARG* 6.1 0.4 - - - +
23Z VAL* 4.1 28.3 - - + -
75Z ARG* 2.8 22.5 + - + +
77Z ILE* 3.4 29.8 - - + -
113Z VAL* 3.8 14.6 - - + -
157Z ILE* 3.0 27.6 + - + +
158Z LYS 2.8 7.8 + - - +
160Z ALA* 1.3 76.9 - - - +
162Z ARG* 1.3 60.0 + - - +
1010Z K 2.7 17.7 - - - -
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Residues in contact with ARG 162 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z GLU* 2.4 47.9 + - - -
19Z ARG* 3.6 47.0 - - - +
75Z ARG* 3.1 13.4 + - - +
158Z LYS* 3.0 23.9 + - - +
159Z SER* 4.0 6.5 - - - +
161Z ILE* 1.3 77.0 - - + +
163Z ASP* 1.3 63.6 + - - +
164Z ASN* 3.3 6.2 + - - +
189Z LYS 4.6 4.6 + - - -
190Z ASP* 5.1 13.5 + - - +
192Z LEU* 4.3 30.9 - - + +
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Residues in contact with ASP 163 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341Y SER 4.9 0.2 - - - +
343Y ASP* 4.7 4.7 - - - +
75Z ARG* 4.0 0.7 - - - -
143Z LYS* 2.6 39.9 + - - +
159Z SER 3.0 19.9 + - - +
160Z ALA 3.6 6.0 - - - +
161Z ILE 3.2 0.6 - - - -
162Z ARG* 1.3 77.2 - - - +
164Z ASN* 1.3 61.9 + - - +
165Z ASN* 2.8 42.3 + - - +
167Z VAL* 4.3 9.9 - - + -
195Z ILE* 4.3 7.2 - - + +
1010Z K 2.3 31.7 - - - -
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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