Contacts of the helix formed by residues 149 - 163 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L VAL* 3.9 5.2 - - - -
148L TRP* 1.3 104.0 - - + +
150L SER* 1.3 66.4 + - - +
151L GLU* 3.0 14.7 + - - +
152L ASP* 2.8 31.1 + - - -
153L ALA* 2.8 22.9 + - - +
180L PHE* 3.4 35.7 - - + -
199L LYS* 5.2 3.2 - - - +
201L GLU* 3.8 8.9 + - - -
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Residues in contact with SER 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L VAL* 2.8 44.6 + - - -
4L THR 3.4 12.5 - - - -
5L VAL* 3.5 7.2 + - - +
8L ALA* 3.6 14.7 - - - +
149L ASN* 1.3 71.8 - - - +
151L GLU* 1.3 66.0 + - - +
153L ALA* 3.1 1.7 + - - -
154L LYS* 2.7 23.2 + - - +
180L PHE* 3.6 19.4 - - - -
182L PHE* 3.9 9.2 - - - -
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Residues in contact with GLU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L ASN* 3.0 13.5 + - - +
150L SER* 1.3 77.9 - - - +
152L ASP* 1.3 65.7 + - - +
155L GLY 2.9 20.6 + - - -
180L PHE* 5.6 0.4 - - - +
181L GLU 4.6 3.6 + - - +
182L PHE* 3.9 9.3 - - + -
183L PRO* 3.3 34.8 - - + +
185L GLU* 4.3 5.4 - - - +
186L ALA* 4.0 11.4 - - + -
191L PHE* 3.3 34.1 - - + -
193L ILE* 3.5 3.4 - - + +
199L LYS* 5.0 13.9 + - - -
239L ARG* 5.1 7.3 + - - +
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Residues in contact with ASP 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L PRO* 3.8 6.7 - - + -
148L TRP* 2.7 31.3 + - - +
149L ASN* 2.8 35.6 + - - +
151L GLU* 1.3 73.1 - - - +
153L ALA* 1.3 60.7 + - - +
156L LEU* 2.7 38.0 + - + +
193L ILE* 3.4 10.5 - - - -
199L LYS* 4.7 1.4 - - - -
201L GLU* 4.3 3.1 - - - +
237L ASN* 3.0 23.2 - - - +
239L ARG* 3.5 28.1 + - - -
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Residues in contact with ALA 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L VAL* 3.7 27.4 - - + +
8L ALA* 4.8 0.2 - - + -
9L ILE* 3.8 18.8 - - + +
147L PRO* 3.5 24.4 - - + +
149L ASN 2.8 15.7 + - - +
150L SER* 3.8 2.2 - - - +
152L ASP* 1.3 79.0 - - - +
154L LYS* 1.3 64.0 + - - +
157L ILE* 3.3 22.9 + - - +
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Residues in contact with LYS 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ALA* 3.7 29.5 - - + +
11L GLN* 2.5 30.1 + - + +
12L GLY* 4.0 5.8 - - - +
15L GLU* 3.2 26.9 + - - -
150L SER 2.7 20.1 + - - +
151L GLU 4.0 1.6 - - - +
153L ALA* 1.3 72.0 - - - +
155L GLY* 1.3 58.8 + - - +
157L ILE* 2.9 26.9 - - - +
158L LYS* 3.2 21.7 - - + +
182L PHE* 3.9 15.7 - - + -
186L ALA 3.0 11.3 + - - +
187L GLN 3.6 0.6 + - - -
188L SER 2.9 26.5 + - - -
191L PHE* 4.1 8.7 - - + -
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Residues in contact with GLY 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L GLU 2.9 11.3 + - - -
154L LYS* 1.3 75.2 - - - +
156L LEU* 1.3 65.0 + - - +
158L LYS* 3.6 1.6 + - - +
159L SER* 3.3 17.0 + - - -
191L PHE* 3.7 16.3 - - - -
192L LEU* 4.1 0.2 - - - -
193L ILE* 3.3 41.1 + - - -
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Residues in contact with LEU 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L VAL* 4.0 34.1 - - + -
147L PRO* 3.8 32.5 - - + -
152L ASP* 2.7 31.2 + - + +
153L ALA 4.4 0.9 - - - +
155L GLY* 1.3 75.0 - - - +
157L ILE* 1.3 58.5 + - - +
158L LYS 2.9 0.7 + - - -
159L SER* 3.2 2.6 + - - -
160L ALA* 2.7 32.0 + - - +
169L VAL* 5.3 1.6 - - + -
193L ILE* 4.1 25.8 - - + +
194L PRO 4.8 2.2 - - - +
195L ILE* 4.4 10.1 - - + +
239L ARG* 4.3 23.1 - - + +
240L THR* 4.5 5.8 - - - +
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Residues in contact with ILE 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ILE* 4.4 12.1 - - + +
12L GLY* 4.2 12.6 - - - -
13L MET* 4.2 18.2 - - + +
77L ILE* 5.1 1.6 - - + -
113L VAL* 4.7 13.0 - - + -
115L ARG* 3.7 37.0 - - + -
153L ALA 3.3 14.6 + - - +
154L LYS* 2.9 27.6 - - - +
156L LEU* 1.3 76.5 - - - +
158L LYS* 1.3 64.3 + - + +
160L ALA* 3.4 5.3 - - - +
161L ILE* 3.0 43.8 + - + +
169L VAL* 4.7 12.0 - - + +
171L GLU* 4.5 5.6 - - - +
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Residues in contact with LYS 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY* 3.7 16.4 - - - +
15L GLU* 3.1 23.2 + - - +
16L GLU* 2.7 39.0 + - - +
154L LYS* 3.2 42.1 + - + +
155L GLY 3.9 3.6 - - - +
156L LEU 2.9 3.0 + - - -
157L ILE* 1.3 73.4 - - + +
159L SER* 1.3 56.3 - - - +
160L ALA 3.0 1.2 + - - -
161L ILE* 3.1 5.4 + - - +
162L ARG* 2.8 45.1 + - - +
189L LYS 4.0 10.2 + - - -
191L PHE 2.8 35.2 - - - +
192L LEU* 3.7 12.3 - - + -
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Residues in contact with SER 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L GLY 3.3 3.4 + - - -
156L LEU 3.2 7.8 + - - -
158L LYS* 1.3 77.0 - - - +
160L ALA* 1.3 61.5 + - - +
162L ARG* 3.6 7.9 - - - +
163L ASP* 3.0 24.9 + - - +
192L LEU* 3.7 15.3 - - - +
193L ILE 2.7 39.8 + - - -
194L PRO* 4.3 2.1 - - - +
195L ILE* 4.2 16.4 - - - +
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Residues in contact with ALA 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L VAL* 3.8 13.4 - - + +
145L VAL* 5.7 1.3 - - + -
156L LEU 2.7 20.5 + - - +
157L ILE* 3.4 11.4 - - - +
158L LYS 3.0 0.2 - - - -
159L SER* 1.3 68.4 - - - +
161L ILE* 1.3 68.2 + - - +
163L ASP* 3.0 18.0 + - - +
167L VAL* 4.2 14.9 - - + +
169L VAL* 4.1 22.0 - - + -
195L ILE* 4.4 10.8 - - + -
1011L K 3.1 8.7 - - - -
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Residues in contact with ILE 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L MET* 4.6 5.4 - - - -
16L GLU* 3.6 40.4 - - + +
19L ARG* 5.8 2.0 - - - +
23L VAL* 3.9 26.7 - - + -
75L ARG* 3.5 15.9 + - + +
77L ILE* 3.4 37.5 - - + -
113L VAL* 3.7 9.1 - - + +
157L ILE* 3.0 30.5 + - + +
158L LYS 3.4 7.0 - - - +
160L ALA* 1.3 78.7 - - - +
162L ARG* 1.3 59.7 + - - +
1011L K 2.8 18.7 - - - -
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Residues in contact with ARG 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLU* 2.5 46.0 + - - -
19L ARG* 3.4 49.1 - - - +
75L ARG* 3.1 15.3 + - - +
158L LYS* 2.8 33.1 + - - +
159L SER* 3.6 9.0 - - - +
160L ALA 3.1 0.2 + - - -
161L ILE* 1.3 72.9 - - - +
163L ASP* 1.3 61.5 + - - +
164L ASN* 3.7 5.5 + - - +
189L LYS* 4.9 3.8 + - - +
190L ASP* 4.5 15.0 + - - +
192L LEU* 3.7 34.6 - - + +
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Residues in contact with ASP 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343K ASP* 4.4 4.3 - - - +
75L ARG* 3.5 2.9 + - - -
111L PRO* 4.5 0.2 - - - +
143L LYS* 2.8 32.8 + - - +
159L SER 3.0 12.8 + - - +
160L ALA* 3.0 13.5 + - - +
162L ARG* 1.3 77.9 - - - +
164L ASN* 1.3 59.1 + - - +
165L ASN* 2.9 43.2 + - - +
167L VAL* 3.9 11.6 - - + +
195L ILE* 4.5 7.9 - - + +
1011L K 2.6 26.5 - - - -
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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
------------------------------------------------------------
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