Contacts of the helix formed by residues 149 - 163 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P VAL* 3.9 5.2 - - - -
148P TRP* 1.3 109.9 - - + +
150P SER* 1.3 55.2 + - - +
151P GLU* 3.4 13.9 + - - +
152P ASP* 2.9 24.6 + - - +
153P ALA* 2.8 34.0 + - - +
180P PHE* 3.4 37.5 - - + -
199P LYS* 5.9 2.0 - - - +
201P GLU* 4.1 8.7 + - - -
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Residues in contact with SER 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P VAL 2.7 27.9 + - - -
4P THR 3.2 14.9 - - - -
5P VAL* 3.4 6.6 + - - +
8P ALA* 3.4 17.4 - - - +
149P ASN* 1.3 72.3 - - - +
151P GLU* 1.3 68.1 + - - +
153P ALA* 2.9 13.2 + - - -
154P LYS* 2.9 12.0 + - - +
180P PHE* 3.4 19.0 - - - -
182P PHE* 3.8 19.7 - - - -
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Residues in contact with GLU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P ASN* 3.4 15.2 + - - +
150P SER* 1.3 76.9 - - - +
152P ASP* 1.3 62.8 + - - +
154P LYS* 3.6 0.5 + - - -
155P GLY 3.3 6.8 + - - -
180P PHE* 5.4 1.5 - - + +
181P GLU 4.3 6.5 + - - +
182P PHE* 3.8 13.7 - - + -
183P PRO* 3.3 31.7 - - + +
186P ALA* 4.6 7.2 - - + -
191P PHE* 3.2 41.4 - - + -
193P ILE* 3.6 5.6 - - + +
199P LYS* 3.9 23.2 - - - -
239P ARG* 5.1 2.1 + - - -
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Residues in contact with ASP 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P PRO* 4.0 5.3 - - + -
148P TRP* 3.0 34.5 + - - +
149P ASN* 2.9 28.8 + - - +
151P GLU* 1.3 70.8 - - - +
153P ALA* 1.3 68.4 + - - +
155P GLY* 3.4 0.5 + - - -
156P LEU* 2.9 32.4 + - + +
193P ILE* 3.6 7.4 - - - -
199P LYS* 4.8 0.9 - - - +
201P GLU* 4.7 2.9 - - - +
237P ASN* 3.5 16.4 + - - +
239P ARG* 3.0 39.6 + - - +
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Residues in contact with ALA 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P VAL* 3.5 27.8 - - + -
8P ALA* 4.3 2.2 - - + -
9P ILE* 3.8 18.8 - - + +
147P PRO* 3.6 19.6 - - + +
149P ASN 2.8 15.9 + - - +
150P SER 2.9 8.0 + - - +
152P ASP* 1.3 73.7 - - - +
154P LYS* 1.3 63.3 + - - +
156P LEU* 4.5 0.3 - - - +
157P ILE* 3.3 24.3 + - - +
169P VAL* 6.1 0.7 - - - +
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Residues in contact with LYS 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ALA* 3.7 27.3 - - + +
11P GLN* 2.7 31.2 + - + +
12P GLY 4.1 4.5 - - - +
15P GLU* 3.3 27.4 + - - -
150P SER 2.9 12.9 + - - +
151P GLU 4.2 2.9 - - - +
153P ALA* 1.3 77.5 - - - +
155P GLY* 1.3 62.7 - - - +
157P ILE* 2.8 25.5 - - - +
158P LYS* 3.1 20.4 + - + +
182P PHE* 3.8 14.5 - - + -
186P ALA 2.7 26.2 + - - +
187P GLN* 3.4 16.4 + - - +
188P SER 3.7 3.0 + - - -
191P PHE* 4.7 5.4 - - + -
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Residues in contact with GLY 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P GLU 3.3 9.1 + - - -
154P LYS* 1.3 79.7 - - - +
156P LEU* 1.3 56.6 + - - +
158P LYS* 3.7 2.0 + - - +
159P SER* 2.9 31.2 + - - -
191P PHE* 4.0 16.6 - - - -
192P LEU 4.2 1.3 - - - -
193P ILE* 3.1 33.7 + - - -
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Residues in contact with LEU 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145P VAL* 4.1 27.7 - - + +
147P PRO* 4.0 30.7 - - + -
152P ASP* 2.9 22.9 + - + +
153P ALA 4.5 1.1 - - - +
155P GLY* 1.3 72.3 - - - +
157P ILE* 1.3 62.3 + - - +
158P LYS 3.2 1.1 - - - -
159P SER* 4.2 1.1 - - - -
160P ALA* 2.7 35.0 + - - +
169P VAL* 4.8 3.8 - - + +
193P ILE* 3.9 31.4 - - + +
194P PRO 4.6 3.6 - - - +
195P ILE* 4.4 18.9 - - + +
239P ARG* 4.4 25.6 - - + +
240P THR* 5.0 1.1 - - - +
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Residues in contact with ILE 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P ILE* 4.4 17.5 - - + +
12P GLY* 4.2 13.2 - - - -
13P MET* 4.2 20.9 - - + -
77P ILE* 5.3 0.9 - - + -
113P VAL* 4.3 13.0 - - + -
115P ARG* 4.1 23.1 - - - -
153P ALA 3.3 14.7 + - - +
154P LYS* 2.8 28.7 - - - +
156P LEU* 1.3 78.4 - - - +
158P LYS* 1.3 68.3 + - + +
160P ALA* 4.2 0.4 - - + -
161P ILE* 3.1 38.2 + - + +
169P VAL* 4.1 26.7 - - + +
171P GLU* 5.3 0.2 - - - +
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Residues in contact with LYS 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P GLY* 3.7 22.4 - - - +
15P GLU* 2.7 38.8 + - - +
16P GLU* 3.4 31.1 + - - +
154P LYS* 3.1 25.1 + - + +
155P GLY 4.0 1.6 - - - +
157P ILE* 1.3 82.6 - - - +
159P SER* 1.3 59.2 + - - +
161P ILE* 3.2 4.2 + - - +
162P ARG* 2.9 35.7 + - - +
189P LYS 2.8 23.0 + - - -
190P ASP 4.4 0.4 - - - -
191P PHE 3.0 31.6 - - - +
192P LEU* 3.7 18.6 - - + -
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Residues in contact with SER 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155P GLY 2.9 13.0 + - - -
156P LEU 4.2 1.6 - - - -
158P LYS* 1.3 75.9 - - - +
160P ALA* 1.3 53.6 + - - +
162P ARG* 3.6 6.8 - - - +
163P ASP* 2.7 37.6 + - - +
192P LEU* 3.6 13.6 - - - +
193P ILE 2.7 34.6 + - - -
194P PRO* 4.7 1.1 - - - +
195P ILE* 4.0 17.0 - - - -
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Residues in contact with ALA 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P VAL* 3.4 14.8 - - + +
145P VAL* 5.5 0.2 - - + -
156P LEU 2.7 23.8 + - - +
157P ILE 3.7 4.5 - - - +
159P SER* 1.3 72.2 - - - +
161P ILE* 1.3 59.5 + - - +
163P ASP* 3.1 12.5 + - - +
167P VAL* 3.4 33.9 - - + +
169P VAL* 3.9 15.0 - - + -
195P ILE* 4.0 5.7 - - + +
1012P K 2.8 16.5 - - - -
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Residues in contact with ILE 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P MET* 4.5 7.4 - - - -
16P GLU* 3.7 39.7 - - + +
19P ARG* 6.1 0.2 - - - +
23P VAL* 3.9 22.7 - - + -
75P ARG* 3.4 17.2 + - + +
77P ILE* 3.5 35.2 - - + -
113P VAL* 3.8 8.5 - - + -
157P ILE* 3.1 34.4 + - + +
158P LYS 3.6 3.4 - - - +
160P ALA* 1.3 75.2 - - - +
162P ARG* 1.3 59.9 + - + +
1012P K 2.9 16.3 - - - -
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Residues in contact with ARG 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 2.7 45.4 + - - -
19P ARG* 3.3 54.6 - - - +
75P ARG* 3.1 14.1 + - - +
158P LYS* 2.9 25.5 + - - +
159P SER* 3.8 7.0 - - - +
161P ILE* 1.3 75.2 - - + +
163P ASP* 1.3 66.6 + - - +
164P ASN* 3.6 4.9 + - - -
189P LYS 4.9 1.2 + - - -
190P ASP* 4.6 18.6 + - - +
192P LEU* 3.8 35.2 - - + +
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Residues in contact with ASP 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343O ASP* 3.9 9.3 - - - +
75P ARG* 3.4 2.3 + - - -
143P LYS* 3.2 34.4 + - - +
159P SER 2.7 22.8 + - - +
160P ALA 3.1 7.7 + - - +
162P ARG* 1.3 74.7 - - - +
164P ASN* 1.3 59.5 + - - +
165P ASN* 3.0 43.7 + - - +
167P VAL* 4.0 9.3 - - + +
195P ILE* 4.4 6.7 - - + +
1012P K 2.6 27.4 - - - -
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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