Contacts of the helix formed by residues 160 - 175 (chain A) in PDB entry 2M8N
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 PRO 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LYS 3.5 8.0 - - - +
159A GLU* 1.3 88.9 - - + +
161A PHE* 1.3 65.8 + - - +
162A ARG* 4.5 6.5 - - + +
163A ASP* 3.0 27.5 + - + +
164A TYR 3.2 8.1 + - - -
220A GLY 6.0 3.1 - - - +
221A VAL* 6.1 1.3 - - + -
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Residues in contact with PHE 161 (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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155A GLN* 3.2 22.8 - - - +
159A GLU 3.2 2.8 + - - -
160A PRO* 1.3 71.9 - - - +
162A ARG* 1.3 56.8 + - - +
164A TYR* 3.2 25.2 + + - +
165A VAL* 2.9 57.2 + - + +
190A LEU* 4.6 14.4 - - + -
191A VAL* 6.0 1.1 - - + -
194A ALA* 4.3 3.4 - - + -
198A CYS* 3.3 32.5 - - - -
202A LEU* 4.5 15.0 - - + -
211A LEU* 5.2 1.6 - - + -
214A MET* 4.2 9.0 - - + -
215A MET* 4.0 34.3 - - + +
218A CYS* 3.8 26.6 + - + +
219A GLN* 5.7 2.1 - - - +
221A VAL* 5.4 1.0 - - - +
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Residues in contact with ARG 162 (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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160A PRO* 3.2 5.4 - - + +
161A PHE* 1.3 80.6 - - - +
163A ASP* 1.3 55.9 + - - +
165A VAL* 3.7 9.2 + - + +
166A ASP* 3.1 25.5 + - - +
215A MET* 4.2 31.9 - - + +
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Residues in contact with ASP 163 (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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159A GLU* 2.7 27.8 - - + +
160A PRO* 3.0 23.4 + - + +
162A ARG* 1.3 75.8 - - - +
164A TYR* 1.3 65.6 + - - +
166A ASP* 3.3 9.8 + - - +
167A ARG* 3.0 33.4 + - - +
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Residues in contact with TYR 164 (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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153A ILE* 3.8 21.0 + - + -
155A GLN* 3.3 34.3 - - + -
159A GLU* 3.1 23.4 + - - +
160A PRO 3.2 4.4 + - - +
161A PHE* 3.6 31.0 - + - +
163A ASP* 1.3 77.2 - - - +
165A VAL* 1.3 58.1 + - - +
167A ARG* 3.2 22.2 + - - +
168A PHE* 2.8 34.3 + + - +
190A LEU* 2.6 52.2 + - + +
193A ASN* 3.1 24.0 - - - +
194A ALA* 4.0 6.1 - - - -
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Residues in contact with VAL 165 (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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161A PHE* 2.9 55.6 + - + +
162A ARG* 3.7 9.4 - - + +
164A TYR* 1.3 75.4 - - - +
166A ASP* 1.3 63.2 + - - +
168A PHE* 3.3 7.4 + - + +
169A TYR* 2.9 28.3 + - + +
190A LEU* 4.5 18.2 - - + -
211A LEU* 5.8 10.1 - - + -
215A MET* 5.8 2.0 - - + -
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Residues in contact with ASP 166 (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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162A ARG 3.1 15.0 + - - +
163A ASP* 3.5 14.5 - - - +
164A TYR 3.3 0.4 - - - -
165A VAL* 1.3 78.3 - - - +
167A ARG* 1.3 58.7 + - + +
169A TYR* 3.8 4.0 - - - +
170A LYS* 2.9 60.3 + - - +
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Residues in contact with ARG 167 (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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153A ILE* 3.4 35.0 - - + +
154A ARG 3.1 22.8 + - - +
159A GLU* 2.5 45.0 + - - -
163A ASP* 3.0 19.9 + - - +
164A TYR* 3.4 19.3 - - - +
166A ASP* 1.3 80.9 - - + +
168A PHE* 1.3 64.4 + - - +
170A LYS* 3.7 6.2 - - - +
171A THR* 2.9 29.8 + - - +
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Residues in contact with PHE 168 (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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150A ILE* 3.2 36.9 - - + +
153A ILE* 4.0 21.9 - - + +
164A TYR* 2.8 26.7 + + + +
165A VAL 3.4 4.9 - - - +
167A ARG* 1.3 78.3 - - - +
169A TYR* 1.3 63.6 + + + +
171A THR* 3.3 4.0 + - - -
172A LEU* 2.9 37.0 + - + +
185A MET* 3.1 37.7 - - + -
186A THR* 4.4 6.1 - - + -
189A LEU* 4.2 6.5 - - + -
190A LEU* 3.6 44.9 - - + -
193A ASN* 4.7 3.1 - - - -
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Residues in contact with TYR 169 (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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165A VAL* 2.9 20.0 + - + +
166A ASP* 4.0 3.8 - - - +
168A PHE* 1.3 79.2 - + + +
170A LYS* 1.3 65.3 - - - +
172A LEU* 3.3 27.3 - - + +
173A ARG* 2.8 73.7 + - + +
186A THR* 5.2 5.8 - - + -
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Residues in contact with LYS 170 (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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166A ASP* 2.9 52.3 + - - +
167A ARG* 3.7 7.2 - - - +
169A TYR* 1.3 83.0 - - - +
171A THR* 1.3 62.7 + - - +
173A ARG* 3.4 33.3 + - - +
174A ALA* 3.3 22.5 + - - +
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Residues in contact with THR 171 (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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148A THR 4.9 0.4 - - - +
149A SER* 2.9 40.6 + - - +
150A ILE* 3.8 10.5 - - + +
153A ILE* 3.8 23.0 - - + +
167A ARG* 2.9 18.6 + - - +
168A PHE 3.4 4.3 - - - -
170A LYS* 1.3 77.9 - - - +
172A LEU* 1.3 63.3 + - - +
174A ALA* 3.3 13.1 + - - +
175A GLU* 3.4 12.0 + - - +
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Residues in contact with LEU 172 (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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149A SER 5.5 0.2 - - - -
150A ILE* 5.3 4.5 - - + +
168A PHE* 2.9 22.6 + - + +
169A TYR* 3.3 30.7 - - + +
171A THR* 1.3 76.5 - - - +
173A ARG* 1.3 65.2 + - - +
175A GLU* 3.2 24.5 + - - +
182A LYS* 3.8 29.8 - - + +
185A MET* 3.2 37.7 - - + -
186A THR* 3.5 31.9 - - + -
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Residues in contact with ARG 173 (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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169A TYR* 2.8 58.1 + - + +
170A LYS* 3.6 41.4 - - - +
171A THR 3.4 0.2 - - - -
172A LEU* 1.3 75.2 - - - +
174A ALA* 1.3 59.7 + - - +
175A GLU 3.4 6.1 + - - +
182A LYS* 6.0 0.9 - - - -
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Residues in contact with ALA 174 (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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170A LYS 3.3 15.6 + - - +
171A THR* 3.9 6.1 - - - +
172A LEU 3.2 1.2 - - - -
173A ARG* 1.3 74.7 - - - +
175A GLU* 1.3 62.7 + - - +
176A GLN* 3.9 0.9 + - - +
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Residues in contact with GLU 175 (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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149A SER* 4.0 18.5 - - - +
150A ILE* 3.9 16.1 - - - +
171A THR 3.4 9.1 + - - +
172A LEU* 3.2 16.8 + - - +
173A ARG 3.8 7.1 - - - +
174A ALA* 1.3 81.8 - - - +
176A GLN* 1.3 73.8 + - - +
177A ALA* 3.3 25.0 + - + +
181A VAL* 5.4 0.3 - - - +
182A LYS* 5.4 4.5 - - + +
185A MET* 3.3 31.0 - - - +
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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
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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