Contacts of the helix formed by residues 149 - 163 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H VAL* 3.7 5.2 - - - -
148H TRP* 1.3 110.5 - - + +
150H SER* 1.3 60.3 + - - +
151H GLU* 3.2 11.7 + - - +
152H ASP* 2.9 30.7 + - - +
153H ALA* 2.9 28.6 + - - +
180H PHE* 3.4 39.9 - - + -
199H LYS* 5.5 3.2 - - - +
201H GLU* 3.7 7.3 + - - -
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Residues in contact with SER 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H VAL* 3.1 17.7 + - - -
4H THR 3.2 1.9 - - - -
5H VAL* 3.0 30.5 + - - +
8H ALA* 3.6 10.5 - - - +
149H ASN* 1.3 73.8 - - - +
151H GLU* 1.3 68.8 + - - +
153H ALA* 2.8 14.0 + - - -
154H LYS* 2.9 11.3 + - - +
180H PHE* 3.6 22.5 - - - -
182H PHE* 3.7 20.4 - - - -
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Residues in contact with GLU 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ASN* 3.5 11.4 - - - +
150H SER* 1.3 78.6 - - - +
152H ASP* 1.3 62.7 + - - +
154H LYS* 3.5 0.5 + - - -
155H GLY 3.1 18.5 + - - -
180H PHE* 5.4 0.6 - - - +
181H GLU 4.9 3.6 + - - +
182H PHE* 3.6 14.4 - - + -
183H PRO* 3.3 32.5 - - + +
185H GLU* 5.9 0.7 - - - -
186H ALA* 4.3 5.4 - - + -
191H PHE* 3.2 35.8 - - + -
193H ILE* 3.7 3.8 - - + +
199H LYS* 4.0 23.4 + - - -
239H ARG* 4.7 4.0 + - - -
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Residues in contact with ASP 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PRO* 3.9 6.9 - - + +
148H TRP* 3.2 23.1 + - - +
149H ASN* 2.9 35.3 + - - +
151H GLU* 1.3 71.2 - - - +
153H ALA* 1.3 62.9 + - - +
156H LEU* 2.8 40.4 + - + +
193H ILE* 3.7 8.7 - - - -
199H LYS* 4.6 3.8 - - - +
237H ASN* 2.8 24.4 - - - +
239H ARG* 3.0 33.3 + - - -
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Residues in contact with ALA 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H VAL* 3.5 27.1 - - + -
8H ALA* 4.8 1.6 - - + -
9H ILE* 3.8 19.1 - - + +
147H PRO* 3.6 21.9 - - + +
149H ASN 2.9 11.8 + - - +
150H SER* 2.8 8.1 + - - +
152H ASP* 1.3 76.8 - - - +
154H LYS* 1.3 59.5 + - - +
156H LEU* 4.3 0.2 - - - +
157H ILE* 3.2 30.1 + - - +
169H VAL* 6.0 0.9 - - - +
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Residues in contact with LYS 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ALA* 3.3 33.4 - - + +
11H GLN* 2.7 31.6 + - - +
12H GLY 4.1 3.8 - - - +
15H GLU* 3.0 33.4 + - - -
150H SER 2.9 9.3 + - - +
151H GLU 4.2 2.2 - - - +
153H ALA* 1.3 76.2 - - - +
155H GLY* 1.3 61.5 + - - +
157H ILE* 3.1 23.2 - - - +
158H LYS* 3.3 19.1 + - + +
182H PHE* 3.7 16.6 - - + -
186H ALA 3.0 23.2 + - - +
187H GLN* 3.3 6.7 + - - +
188H SER 3.2 12.3 + - - -
191H PHE* 4.6 4.9 - - + -
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Residues in contact with GLY 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H GLU 3.1 11.1 + - - -
154H LYS* 1.3 76.3 - - - +
156H LEU* 1.3 56.6 + - - +
158H LYS* 3.9 0.6 - - - -
159H SER* 3.1 20.4 + - - -
191H PHE* 3.7 26.3 - - - -
192H LEU* 3.9 1.2 - - - -
193H ILE* 3.1 36.5 + - - -
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H VAL* 3.9 32.8 - - + +
147H PRO* 4.0 26.7 - - + -
152H ASP* 2.8 21.8 + - - +
153H ALA 4.3 1.6 - - - +
155H GLY* 1.3 74.1 - - - +
157H ILE* 1.3 55.9 + - - +
158H LYS 3.1 1.6 - - - -
159H SER* 3.4 1.6 + - - -
160H ALA* 2.7 37.5 + - - +
169H VAL* 5.1 1.1 - - + +
193H ILE* 3.7 33.7 - - + +
194H PRO 4.8 2.9 - - - +
195H ILE* 4.6 8.9 - - + +
239H ARG* 3.7 37.7 - - + +
240H THR* 5.1 0.7 - - - +
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Residues in contact with ILE 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 4.4 14.4 - - + +
12H GLY* 4.4 11.2 - - - -
13H MET* 4.2 20.0 - - + -
77H ILE* 5.2 0.9 - - + -
113H VAL* 4.1 19.7 - - + -
115H ARG* 3.8 28.3 - - + +
153H ALA 3.2 15.0 + - - +
154H LYS* 3.1 18.6 - - - +
156H LEU* 1.3 79.7 - - - +
158H LYS* 1.3 67.0 + - + +
160H ALA* 4.2 2.2 - - + -
161H ILE* 3.1 35.3 + - + +
169H VAL* 4.3 16.6 - - + +
171H GLU* 4.9 1.6 - - - +
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Residues in contact with LYS 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H GLY* 3.7 24.0 - - - +
15H GLU* 2.6 37.6 + - - +
16H GLU* 3.5 27.7 + - - +
154H LYS* 3.3 27.2 + - + +
155H GLY 4.2 0.7 - - - +
156H LEU 3.1 0.6 - - - -
157H ILE* 1.3 81.4 - - + +
159H SER* 1.3 65.9 + - - +
161H ILE* 3.1 3.6 + - - +
162H ARG* 2.8 28.6 + - - +
189H LYS 3.2 23.4 + - - -
191H PHE 2.9 30.3 - - - +
192H LEU* 4.0 9.2 - - + -
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Residues in contact with SER 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H GLY 3.1 14.2 + - - -
156H LEU 3.8 3.1 - - - -
158H LYS* 1.3 75.7 - - - +
160H ALA* 1.3 62.5 + - - +
162H ARG* 3.4 7.5 + - - +
163H ASP* 2.9 23.2 + - - +
192H LEU* 3.6 16.6 - - - +
193H ILE 2.9 35.7 + - - -
194H PRO* 4.2 2.5 - - - +
195H ILE* 4.3 17.5 - - - +
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Residues in contact with ALA 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 3.7 13.9 - - + +
145H VAL* 5.5 0.7 - - + -
156H LEU 2.7 21.7 + - - +
157H ILE* 3.8 5.4 - - - +
159H SER* 1.3 72.2 - - - +
161H ILE* 1.3 51.7 + - - +
163H ASP* 2.8 15.2 + - - +
167H VAL* 3.6 35.5 - - + +
169H VAL* 3.9 13.9 - - + -
195H ILE* 4.4 5.0 - - + +
1013H K 2.7 23.9 - - - -
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Residues in contact with ILE 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H GLY 4.8 0.2 - - - +
13H MET* 4.6 8.1 - - + -
16H GLU* 3.8 42.6 - - + +
19H ARG* 5.8 0.7 - - - +
23H VAL* 4.3 21.3 - - + -
75H ARG* 3.4 19.0 + - + +
77H ILE* 3.4 33.0 - - + -
113H VAL* 3.9 14.6 - - + -
157H ILE* 3.1 32.8 + - + +
158H LYS 3.1 4.3 + - - +
160H ALA* 1.3 74.1 - - - +
162H ARG* 1.3 62.3 + - - +
1013H K 3.2 13.8 - - - -
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Residues in contact with ARG 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLU* 2.2 46.3 + - - -
19H ARG* 3.2 52.2 - - - +
75H ARG* 3.6 10.3 + - - +
158H LYS* 2.8 23.5 + - - +
159H SER* 3.6 8.5 - - - +
161H ILE* 1.3 70.8 - - - +
163H ASP* 1.3 65.4 + - - +
164H ASN* 4.0 2.8 - - - +
189H LYS 4.6 3.6 + - - -
190H ASP* 4.8 15.4 + - - +
192H LEU* 4.0 34.7 - - + +
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Residues in contact with ASP 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G ASP* 4.1 5.9 - - - +
75H ARG* 3.0 14.7 + - - -
111H PRO* 4.2 0.5 - - - +
143H LYS* 2.8 32.8 + - - +
159H SER 2.9 11.2 + - - +
160H ALA* 2.8 19.9 + - - +
162H ARG* 1.3 72.4 - - - +
164H ASN* 1.3 61.4 + - - +
165H ASN* 2.8 45.0 + - - +
167H VAL* 3.9 12.8 - - + +
195H ILE* 4.7 5.4 - - + +
1013H K 2.8 16.0 - - - -
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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
------------------------------------------------------------
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