Contacts of the helix formed by residues 152 - 170 (chain X) in PDB entry 5M32
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 SER 152 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12X TYR* 2.8 11.6 + - - -
151X ILE* 1.3 77.1 - - - +
153X ARG* 1.3 65.3 + - - +
154X GLU* 3.7 17.3 + - - -
155X ARG* 3.3 22.7 + - - +
156X ALA* 3.2 15.2 + - - +
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Residues in contact with ARG 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X ASP* 5.2 4.3 - - - +
12X TYR* 3.4 33.9 - - + -
14X LEU* 4.8 1.0 - - - +
152X SER* 1.3 76.6 - - - +
154X GLU* 1.3 63.9 + - - +
156X ALA* 3.1 5.0 + - - +
157X VAL* 2.9 33.1 + - + +
182X VAL* 3.5 32.6 - - + +
184X ASP* 3.1 29.6 + - - -
189X HIS* 4.9 8.3 + - - +
191X LEU* 5.2 4.9 - - - +
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Residues in contact with GLU 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152X SER* 3.7 16.7 + - - +
153X ARG* 1.3 80.2 + - - +
155X ARG* 1.3 61.2 + - + +
157X VAL* 3.3 9.0 + - - +
158X GLU* 3.0 33.8 + - - +
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Residues in contact with ARG 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X TYR* 3.6 39.8 + - - +
151X ILE* 3.8 19.1 - - + -
152X SER* 3.3 21.2 + - - +
153X ARG 3.3 0.4 - - - -
154X GLU* 1.3 83.9 - - + +
156X ALA* 1.3 56.1 + - - +
158X GLU* 3.3 20.4 + - - +
159X LEU* 2.9 46.8 + - - +
162X LYS* 3.6 25.8 - - - +
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Residues in contact with ALA 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ILE* 4.6 12.5 - - + +
12X TYR* 3.4 26.7 - - + +
14X LEU* 3.8 18.3 - - + +
151X ILE* 3.9 17.9 - - + +
152X SER 3.2 6.4 + - - +
153X ARG 3.1 4.8 + - - +
155X ARG* 1.3 75.8 - - - +
157X VAL* 1.3 61.9 + - - +
159X LEU* 3.6 6.0 - - + +
160X LEU* 2.9 27.5 + - - +
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Residues in contact with VAL 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X LEU* 4.3 11.0 - - + -
153X ARG* 2.9 22.3 + - + +
154X GLU* 3.7 9.9 - - - +
155X ARG 3.3 0.4 - - - -
156X ALA* 1.3 77.7 - - - +
158X GLU* 1.3 58.5 + - - +
160X LEU* 3.1 10.2 + - + +
161X ARG* 2.9 36.4 + - + +
180X VAL* 5.8 3.8 - - + -
182X VAL* 4.9 1.3 - - + -
191X LEU* 3.5 33.4 - - + -
194X ILE* 5.6 6.1 - - + -
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Residues in contact with GLU 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X GLU* 3.0 21.6 + - - +
155X ARG* 3.3 34.2 + - - +
157X VAL* 1.3 75.3 - - - +
159X LEU* 1.3 62.8 + - - +
161X ARG* 3.2 21.5 + - + +
162X LYS* 2.9 39.7 + - - +
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Residues in contact with LEU 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ILE* 5.4 2.9 - - + -
142X ILE* 4.0 20.6 - - + +
143X LEU* 3.7 24.9 - - + -
146X TYR* 3.6 36.8 - - + -
147X TYR* 4.5 14.4 - - + -
151X ILE* 4.1 21.8 - - + -
155X ARG* 2.9 29.0 + - - +
156X ALA* 3.6 6.5 - - + +
158X GLU* 1.3 78.8 - - - +
160X LEU* 1.3 57.4 + - - +
162X LYS* 3.1 14.2 + - + +
163X CYS* 3.0 25.3 + - - -
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Residues in contact with LEU 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ILE* 3.7 29.4 - - + -
7X ILE* 3.7 18.8 - - + -
14X LEU* 3.8 18.2 - - + -
16X ALA* 4.0 15.7 - - + -
156X ALA 2.9 18.2 + - - +
157X VAL* 3.1 8.5 + - + +
159X LEU* 1.3 76.9 - - - +
161X ARG* 1.3 58.6 + - - +
163X CYS* 3.3 11.1 + - + -
164X LEU* 3.0 44.8 + - + +
180X VAL* 4.1 6.1 - - + -
194X ILE* 3.6 25.4 - - + -
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Residues in contact with ARG 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X VAL* 2.9 27.2 + - + +
158X GLU* 3.5 18.8 + - - +
159X LEU 3.2 0.4 - - - -
160X LEU* 1.3 75.2 - - - +
162X LYS* 1.3 59.7 + - - +
164X LEU* 4.2 5.3 - - - +
165X GLU* 2.9 40.0 + - - +
194X ILE* 3.9 32.9 - - + +
196X PHE* 5.0 11.7 - - + -
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Residues in contact with LYS 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ARG* 3.5 48.6 - - + +
142X ILE* 4.4 7.3 - - + +
146X TYR* 4.7 14.4 - - + -
155X ARG* 3.6 29.5 - - - +
158X GLU* 2.9 31.0 + - - +
159X LEU* 3.1 21.7 + - + +
161X ARG* 1.3 76.2 - - - +
163X CYS* 1.3 61.9 + - - +
165X GLU* 3.3 14.3 - - - +
166X GLU* 3.0 25.3 + - - +
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Residues in contact with CYS 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X TYR* 4.5 7.6 - - - +
5X ILE* 5.6 0.2 - - + -
139X THR* 3.2 24.9 + - - +
142X ILE* 3.8 22.9 - - - -
143X LEU* 3.7 36.8 - - - -
159X LEU 3.0 18.3 + - - -
160X LEU* 3.6 16.4 - - + +
162X LYS* 1.3 78.1 - - - +
164X LEU* 1.3 59.2 + - + +
166X GLU* 3.5 1.4 + - - +
167X LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X TYR* 3.7 21.8 - - + +
5X ILE* 5.2 1.8 - - + -
16X ALA* 5.2 0.7 - - + -
160X LEU* 3.0 30.6 + - + +
161X ARG* 4.2 3.4 - - - +
163X CYS* 1.3 75.9 - - - +
165X GLU* 1.3 61.4 + - - +
167X LEU* 3.7 4.3 - - + +
168X GLN* 2.9 26.5 + - - +
178X PHE* 3.6 57.7 - - + -
194X ILE* 3.3 35.7 - - + -
196X PHE* 3.8 16.1 - - + -
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Residues in contact with GLU 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ARG* 3.1 35.6 + - - +
161X ARG* 2.9 26.9 + - - +
162X LYS* 3.3 19.5 - - - +
164X LEU* 1.3 74.8 - - - +
166X GLU* 1.3 60.6 + - - +
168X GLN* 3.3 8.3 + - - +
169X LYS* 3.0 27.7 + - - +
196X PHE* 4.1 16.5 - - + -
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Residues in contact with GLU 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K TYR 3.6 0.7 - - - +
137K GLY* 3.5 28.7 + - - +
140K ASP* 3.3 36.4 - - - +
141K ARG* 4.1 4.2 + - - +
138X LEU* 4.0 12.4 - - + +
139X THR* 5.4 0.7 - - - +
142X ILE* 3.6 23.0 - - + +
162X LYS 3.0 17.2 + - - +
163X CYS 3.8 2.9 - - - +
165X GLU* 1.3 77.5 - - + +
167X LEU* 1.3 59.2 + - - +
169X LYS* 2.9 19.6 + - - +
170X ARG* 3.0 41.6 + - - +
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Residues in contact with LEU 167 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3X TYR* 4.6 18.4 - - + -
135X GLY* 3.7 34.1 - - - +
138X LEU* 3.9 12.7 - - + +
139X THR* 4.8 2.2 - - - -
163X CYS 2.9 18.8 + - - +
164X LEU* 3.8 7.9 - - + +
165X GLU 3.4 0.2 - - - -
166X GLU* 1.3 76.1 - - - +
168X GLN* 1.3 60.7 + - - +
171X PHE* 3.3 41.6 + - + +
173X LEU 5.1 2.3 - - - +
175X LEU* 3.7 32.3 - - + -
178X PHE* 3.7 20.0 - - + -
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Residues in contact with GLN 168 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174J ASN* 2.7 48.2 + - - +
164X LEU 2.9 18.3 + - - +
165X GLU* 3.5 10.5 - - - +
166X GLU 3.1 0.2 - - - -
167X LEU* 1.3 79.9 - - - +
169X LYS* 1.3 55.6 + - - +
173X LEU 5.3 0.7 - - - +
174X ASN* 4.8 6.1 - - - +
175X LEU 3.1 29.4 + - - +
176X PRO* 3.7 8.5 - - - +
178X PHE* 4.8 0.4 - - - -
196X PHE* 3.3 38.0 - - + +
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Residues in contact with LYS 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLN* 2.4 36.4 + - - +
140K ASP* 3.1 40.8 + - - +
143K TYR* 6.1 1.4 - - - -
165X GLU 3.0 14.9 + - - +
166X GLU* 2.9 9.6 + - - +
168X GLN* 1.3 79.2 - - - +
170X ARG* 1.3 68.4 + - + +
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Residues in contact with ARG 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J VAL* 3.5 8.7 - - + -
27J GLN* 2.9 56.7 + - - +
28J MET* 3.9 16.8 + - - +
29J LYS* 4.5 2.6 - - - +
125K THR* 3.5 34.6 + - - +
126K PHE* 6.3 0.2 - - - -
136K TYR* 4.9 27.6 - - + -
139K MET* 5.3 0.4 - - - +
140K ASP* 2.9 32.2 + - - +
138X LEU* 4.3 13.5 - - + -
166X GLU* 3.0 31.9 + - - +
169X LYS* 1.3 90.3 - - + +
171X PHE* 1.3 65.8 + - - +
172X ILE 3.5 0.2 + - - -
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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