Contacts of the helix formed by residues 175 - 199 (chain A) in PDB entry 5M64
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE 3.5 4.6 + - - -
174A SER* 1.3 70.6 - - - +
176A THR* 1.3 63.0 + - - +
177A LEU 3.3 1.3 - - - -
178A LEU* 3.1 17.7 + - - +
179A ASN* 2.8 32.3 + - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.3 9.9 - - - -
175A SER* 1.3 77.5 + - - +
177A LEU* 1.3 62.0 + - - +
179A ASN* 3.0 23.3 + - + +
180A GLU* 3.1 14.7 + - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 6.0 4.5 - - - -
173A ILE* 3.7 29.4 - - + -
174A SER* 3.3 34.6 + - - +
176A THR* 1.3 80.2 - - - +
178A LEU* 1.3 80.2 + - + +
180A GLU* 3.0 36.6 - - + +
181A LEU* 3.2 19.4 + - + +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.6 31.0 - - + -
173A ILE* 3.8 14.1 - - + +
174A SER 3.2 27.6 - - - +
175A SER* 3.1 17.3 + - - +
177A LEU* 1.3 90.2 - - + +
179A ASN* 1.3 65.7 + - - +
181A LEU* 3.3 23.9 + - + +
182A LYS* 3.1 35.4 + - - +
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 2.8 30.9 + - - +
176A THR* 3.0 13.7 + - + +
178A LEU* 1.3 77.8 - - - +
180A GLU* 1.3 57.9 + - - +
182A LYS* 3.2 10.2 + - - +
183A SER* 3.0 26.5 + - - -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.9 16.8 - - - +
142A GLY* 4.6 6.4 - - - -
176A THR* 3.1 7.8 + - + +
177A LEU* 3.0 35.5 - - - +
179A ASN* 1.3 74.1 - - - +
181A LEU* 1.3 75.3 + - - +
183A SER* 3.7 8.9 - - - -
184A LYS* 2.9 28.1 + - - +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 4.8 9.9 - - + -
139A ILE 5.2 2.5 - - - +
140A THR* 5.6 2.0 - - + -
141A LEU* 4.1 19.5 - - + +
177A LEU* 3.2 25.5 + - + +
178A LEU* 3.4 34.3 - - + +
179A ASN 3.2 0.2 - - - -
180A GLU* 1.3 88.0 - - - +
182A LYS* 1.3 64.4 + - - +
184A LYS* 3.1 31.5 + - - +
185A ARG* 2.9 41.2 + - - +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.3 32.4 - - - -
113A VAL* 3.5 35.7 - - - +
116A HIS* 3.6 37.2 + - + +
178A LEU* 3.1 24.7 + - - +
179A ASN* 3.6 11.0 - - - +
181A LEU* 1.3 77.4 - - - +
183A SER* 1.3 63.2 + - - +
185A ARG* 3.1 10.3 + - + +
186A SER* 3.0 22.9 + - - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN 3.0 15.4 + - - -
180A GLU* 3.9 8.7 - - - -
182A LYS* 1.3 76.3 - - - +
184A LYS* 1.3 56.7 + - - +
186A SER* 3.8 6.3 - - - -
187A GLU* 2.9 36.9 + - - +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.2 0.9 + - + -
139A ILE* 3.4 51.8 + - + +
141A LEU* 5.9 6.5 - - + -
180A GLU* 2.9 22.1 + - - +
181A LEU* 3.1 32.4 + - - +
183A SER* 1.3 75.2 - - - +
185A ARG* 1.3 93.5 + - - +
187A GLU* 3.3 21.3 - - + +
188A TYR* 3.0 30.5 + - + +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.1 18.3 + - - +
116A HIS* 3.6 27.1 + - + +
117A ARG* 3.1 79.1 - - - +
120A CYS* 3.6 9.0 - - - -
136A LEU* 4.8 4.7 - - - -
139A ILE 4.7 4.9 + - - -
181A LEU* 2.9 29.8 + - - +
182A LYS* 3.1 9.9 + - + +
184A LYS* 1.3 106.9 - - - +
186A SER* 1.3 56.9 + - - +
188A TYR* 4.8 2.0 - - - -
189A VAL* 3.0 36.3 + - - +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 5.1 2.2 - - - -
120A CYS* 5.4 1.3 - - - -
182A LYS 3.0 14.6 + - - -
183A SER* 3.8 7.2 - - - -
185A ARG* 1.3 78.1 - - - +
187A GLU* 1.3 57.2 + - - +
189A VAL* 5.0 1.8 - - - -
190A ASP* 2.9 39.0 + - - +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 2.9 24.1 + - - +
184A LYS* 3.3 28.2 - - + +
186A SER* 1.3 76.0 - - - +
188A TYR* 1.3 60.6 + - + +
190A ASP* 4.3 3.1 - - - +
191A MET* 3.4 24.3 + - - +
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 5.2 0.4 - - + -
132A GLU* 2.7 31.5 + - + -
135A LYS* 3.5 29.1 + - - +
136A LEU* 3.5 34.3 - - + -
138A GLU* 5.4 0.2 + - - -
139A ILE* 5.4 15.3 - - + -
184A LYS* 3.0 24.8 + - + +
185A ARG* 4.1 2.7 - - - +
187A GLU* 1.3 78.6 - - + +
189A VAL* 1.3 61.8 + - - +
190A ASP 3.3 0.2 - - - -
191A MET* 3.3 4.9 + - + +
192A ALA* 2.8 35.8 + - + +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A CYS* 3.5 23.1 - - - +
123A ARG* 4.6 18.4 - - + +
124A LEU* 4.0 14.4 - - + -
136A LEU* 3.7 30.7 - - + -
185A ARG 3.0 18.0 + - - +
186A SER* 4.3 1.8 - - - +
188A TYR* 1.3 73.0 - - - +
190A ASP* 1.3 61.7 + - - +
192A ALA 4.4 0.2 - - - +
193A ILE* 2.8 48.8 + - + +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 2.9 23.8 + - - +
187A GLU* 4.6 4.0 - - - +
189A VAL* 1.3 78.1 - - - +
191A MET* 1.3 60.5 + - - +
193A ILE* 4.0 6.8 - - - +
194A ALA* 3.0 30.9 + - - +
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Residues in contact with MET 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU 3.4 19.9 + - - +
188A TYR* 3.3 6.1 + - + +
189A VAL 3.2 0.2 - - - -
190A ASP* 1.3 81.5 + - - +
192A ALA* 1.3 59.5 + - - +
194A ALA* 3.3 9.0 + - + +
195A LYS* 3.0 50.1 + - + +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.0 21.1 - - + -
129A LEU* 4.9 4.7 - - + +
132A GLU* 4.6 18.6 - - + +
188A TYR* 2.8 29.7 + - + +
189A VAL 3.9 2.5 - - - +
191A MET* 1.3 74.5 - - - +
193A ILE* 1.3 59.4 + - + +
195A LYS* 3.4 7.9 + - - +
196A ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG 4.6 0.2 - - - +
124A LEU* 3.7 33.7 - - + +
126A GLN* 4.8 3.1 - - - +
127A TYR* 4.2 25.6 - - + +
129A LEU* 5.1 4.7 - - + -
189A VAL* 2.8 43.3 + - + +
190A ASP* 4.3 7.0 - - - +
192A ALA* 1.3 71.3 - - - +
194A ALA* 1.3 62.4 + - - +
196A ALA* 4.3 4.9 - - + -
197A LEU* 2.8 45.0 + - + +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP* 3.0 25.0 + - - +
191A MET* 3.4 14.6 - - + +
192A ALA 3.2 0.2 - - - -
193A ILE* 1.3 79.9 - - - +
195A LYS* 1.3 57.9 + - + +
197A LEU* 3.4 3.9 + - - +
198A SER* 2.9 30.0 + - - -
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A MET* 3.0 40.9 + - + +
192A ALA* 3.9 6.1 - - - +
194A ALA* 1.3 75.0 - - + +
196A ALA* 1.3 62.2 + - - +
198A SER* 3.1 15.0 + - - -
199A ASP* 3.2 22.7 + - - +
201A ARG* 3.8 14.1 + - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.6 30.5 - - + -
192A ALA 2.9 18.3 + - - +
193A ILE* 3.7 6.1 - - + +
195A LYS* 1.3 78.7 - - - +
197A LEU* 1.3 62.3 + - + +
198A SER 3.2 1.0 + - - -
199A ASP 3.8 0.9 + - - -
201A ARG* 3.2 49.1 + - - +
202A THR* 3.5 12.4 + - + +
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 4.1 21.1 - - + +
193A ILE* 2.8 46.1 + - + +
194A ALA* 3.6 4.3 - - - +
196A ALA* 1.3 75.0 - - + +
198A SER* 1.3 60.4 + - - +
200A GLY 5.4 0.6 + - - -
202A THR* 3.3 36.2 - - + +
203A THR* 3.3 25.4 - - - +
204A GLU* 3.8 8.7 - - + +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA 2.9 17.6 + - - -
195A LYS* 3.5 10.5 - - - -
196A ALA 3.1 1.0 - - - -
197A LEU* 1.3 80.8 - - - +
199A ASP* 1.3 76.7 + - - +
200A GLY 3.8 2.8 + - - -
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Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.2 16.4 + - - +
198A SER* 1.3 95.8 + - - +
200A GLY* 1.3 52.9 + - - +
201A ARG* 2.7 28.7 + - - +
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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