Contacts of the helix formed by residues 149 - 163 (chain D) in PDB entry 3EXF
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D VAL* 3.8 5.6 - - - +
148D TRP* 1.3 115.9 - - + +
150D SER* 1.3 58.6 + - - +
151D GLU* 3.0 18.2 + - - +
152D ASP* 2.9 27.4 + - - +
153D ALA* 2.9 28.8 + - - +
180D PHE* 3.6 31.8 - - + -
199D LYS* 5.4 1.2 - - - +
201D GLU* 3.9 12.1 + - - -
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL 2.7 28.2 + - - -
5D VAL* 3.0 23.9 + - - +
8D ALA* 3.5 15.2 - - - +
149D ASN* 1.3 77.0 - - - +
151D GLU* 1.3 65.7 + - - +
153D ALA 3.0 9.9 + - - -
154D LYS* 3.0 13.9 + - - +
180D PHE* 3.8 13.4 - - - -
182D PHE* 3.5 22.8 - - - -
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ASN* 3.0 12.1 + - - +
150D SER* 1.3 75.0 - - - +
152D ASP* 1.3 65.2 + - - +
155D GLY 3.0 20.1 + - - -
180D PHE* 5.7 0.4 - - - +
181D GLU 5.4 2.8 + - - +
182D PHE* 3.6 11.5 - - - -
183D PRO* 4.3 23.6 - - + +
185D GLU* 5.7 2.8 - - - +
186D ALA* 4.2 9.0 - - + -
191D PHE* 3.4 38.6 - - + -
193D ILE* 3.4 3.4 - - + +
199D LYS* 4.8 14.6 + - - +
239D ARG* 4.3 15.8 + - - -
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Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PRO* 3.9 6.4 - - + -
148D TRP* 3.2 28.6 + - - +
149D ASN* 2.9 30.9 + - - +
151D GLU* 1.3 75.8 - - - +
153D ALA* 1.3 52.7 + - - +
155D GLY 3.6 0.2 - - - -
156D LEU* 2.6 40.8 + - + +
193D ILE* 3.8 6.8 - - - +
201D GLU* 4.2 1.6 - - - +
237D ASN* 2.7 24.3 - - - +
239D ARG* 2.7 43.0 + - - +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.5 8.1 - - + -
8D ALA* 4.4 4.9 - - + -
9D ILE* 3.7 27.8 - - + -
147D PRO* 3.9 20.2 - - + -
149D ASN 2.9 18.9 + - - +
150D SER* 3.0 4.7 + - - +
152D ASP* 1.3 69.6 - - - +
154D LYS* 1.3 61.4 + - - +
156D LEU* 4.6 0.2 - - - -
157D ILE* 2.9 37.7 + - + +
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ALA* 3.2 27.0 + - + +
11D GLN* 2.6 28.0 + - - +
12D GLY* 3.7 20.6 - - - +
15D GLU* 3.2 28.7 + - - +
150D SER 3.0 11.4 + - - +
151D GLU 4.6 0.2 - - - +
153D ALA* 1.3 77.6 - - - +
155D GLY* 1.3 62.9 + - - +
157D ILE* 4.0 5.1 - - - +
158D LYS* 3.2 33.6 + - + +
182D PHE* 4.2 9.1 - - + -
186D ALA 3.1 24.7 + - - -
187D GLN 4.1 4.9 + - - -
188D SER 3.7 10.7 + - - -
191D PHE* 4.2 10.3 - - + -
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLU 3.0 12.7 + - - -
154D LYS* 1.3 78.7 - - - +
156D LEU* 1.3 66.4 + - - +
159D SER* 3.5 13.3 + - - -
191D PHE* 3.6 31.1 - - - -
192D LEU* 4.0 0.9 - - - -
193D ILE* 3.2 26.5 + - - -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D VAL* 4.2 33.2 - - + +
147D PRO* 4.0 28.7 - - + -
152D ASP 2.6 25.2 + - - +
153D ALA* 4.1 3.1 - - - +
155D GLY* 1.3 72.9 - - - +
157D ILE* 1.3 59.3 + - + +
159D SER* 3.3 3.5 - - - -
160D ALA* 3.1 26.5 + - - +
193D ILE* 3.6 30.9 - - + +
194D PRO 4.8 1.3 - - - +
195D ILE* 4.3 7.9 - - + +
239D ARG* 3.7 36.3 - - + +
240D THR* 4.7 5.2 - - - +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.3 43.3 - - + +
12D GLY* 3.8 4.0 - - - -
13D MET* 3.5 31.2 - - + +
113D VAL* 6.3 1.6 - - + -
115D ARG* 5.4 5.6 - - + -
147D PRO* 5.5 0.9 - - + -
153D ALA* 2.9 26.8 + - + +
154D LYS* 4.0 5.8 - - - +
156D LEU* 1.3 74.7 - - + +
158D LYS* 1.3 72.8 + - - +
160D ALA* 3.6 8.6 - - + +
161D ILE* 3.1 25.5 + - + +
169D VAL* 3.8 31.0 - - + -
171D GLU* 4.8 3.1 - - + +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY* 3.6 16.2 + - - +
15D GLU* 2.9 47.9 + - - +
16D GLU* 3.3 32.4 + - - +
154D LYS* 3.2 26.7 + - + +
157D ILE* 1.3 80.1 - - - +
159D SER* 1.3 69.6 + - - +
161D ILE* 2.6 22.3 + - - +
162D ARG* 3.2 5.3 + - - +
189D LYS 3.0 25.3 + - - -
190D ASP 4.5 0.7 - - - -
191D PHE 3.2 28.5 - - - +
192D LEU* 4.1 7.2 - - + -
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Residues in contact with SER 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLY 3.5 5.9 + - - -
156D LEU* 3.3 11.4 - - - -
158D LYS* 1.3 72.8 - - - +
160D ALA* 1.3 56.2 + - - -
162D ARG* 2.6 28.3 + - - +
163D ASP* 2.9 11.5 + - - +
192D LEU* 3.8 23.4 - - - +
193D ILE 2.7 36.6 + - - -
194D PRO* 4.4 2.4 - - - +
195D ILE* 4.3 13.1 + - - -
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 3.4 18.8 - - + +
145D VAL* 5.7 0.4 - - + -
156D LEU 3.1 14.6 + - - +
157D ILE* 3.6 10.8 - - - +
158D LYS 3.0 1.0 + - - -
159D SER* 1.3 75.1 - - - +
161D ILE* 1.3 62.2 + - - +
163D ASP* 3.5 13.4 - - - +
167D VAL* 3.6 30.8 - - + +
169D VAL* 4.2 9.6 - - + -
195D ILE* 4.0 7.8 - - + +
1002D K 3.2 12.3 - - - -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY 4.3 6.7 - - - +
13D MET* 4.3 7.0 - - + -
16D GLU* 3.3 51.4 - - + +
23D VAL* 3.8 26.9 - - + -
75D ARG* 2.9 17.1 + - + +
77D ILE* 3.9 30.3 - - + -
113D VAL* 4.5 7.2 - - + -
157D ILE* 3.1 25.4 + - + +
158D LYS 2.6 13.8 + - - +
160D ALA* 1.3 72.5 - - + +
162D ARG* 1.3 54.1 + - - +
1002D K 2.9 21.1 - - - -
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Residues in contact with ARG 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLU* 2.4 37.5 + - - -
19D ARG* 2.9 60.8 - - - +
75D ARG* 3.0 10.6 + - - +
158D LYS* 3.2 9.3 + - - +
159D SER* 2.6 18.3 + - - +
161D ILE* 1.3 72.5 - - - +
163D ASP* 1.3 60.6 + - - +
164D ASN* 3.7 5.5 - - - +
189D LYS 4.3 10.3 + - - -
190D ASP* 4.3 12.3 + - - +
192D LEU* 3.4 41.3 - - + +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ASP* 4.7 2.4 - - - +
75D ARG* 2.4 25.8 + - - -
143D LYS* 2.9 28.7 + - - +
159D SER 2.9 10.5 + - - +
160D ALA* 3.5 15.5 - - - +
162D ARG* 1.3 74.3 - - - +
164D ASN* 1.3 55.5 + - - +
165D ASN* 2.9 42.0 + - - +
167D VAL* 4.0 16.4 - - + -
195D ILE* 4.1 10.5 - - + +
1002D K 3.2 12.9 - - - -
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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
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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