Contacts of the helix formed by residues 170 - 181 (chain A) in PDB entry 1M9H
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 GLN 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.6 6.8 - - - +
162A ILE* 3.6 16.0 - - + +
163A GLU* 2.6 41.4 + - - +
168A TYR* 3.5 44.1 + - + -
169A GLN* 1.4 75.7 - - - +
171A ARG* 1.3 58.1 + - - +
172A GLU* 3.3 3.8 - - - -
173A ILE* 3.0 49.2 + - + +
174A THR* 3.1 9.9 + - - +
262A ASP* 4.4 1.8 + - - -
273A HIS* 6.1 0.2 - - - -
274A PRO* 5.8 2.6 - - - +
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Residues in contact with ARG 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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169A GLN* 2.7 36.3 + - + +
170A GLN* 1.3 72.1 - - - +
172A GLU* 1.3 56.2 + - + +
174A THR* 3.1 11.8 + - - +
175A ASP* 2.7 48.9 + - - +
259A ASP* 2.5 43.8 + - - +
260A ALA* 4.7 0.8 - - - +
262A ASP* 4.1 13.1 + - - +
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Residues in contact with GLU 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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143A VAL* 3.7 13.5 - - + +
170A GLN 3.2 1.7 + - - -
171A ARG* 1.3 76.2 - - + +
173A ILE* 1.3 60.9 + - + +
175A ASP* 3.6 7.1 - - - +
176A TRP* 2.9 28.9 + - - +
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Residues in contact with ILE 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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140A ASN 6.2 0.2 - - - -
141A HIS 3.9 11.0 - - - +
142A LEU* 3.9 22.7 - - + -
143A VAL* 4.0 19.7 - - + +
146A LEU* 4.4 7.2 - - + -
160A ASN* 3.5 26.2 - - + +
162A ILE* 4.1 15.9 - - + -
170A GLN* 3.0 42.5 + - + +
172A GLU* 1.3 76.8 - - + +
174A THR* 1.3 60.9 + - - +
176A TRP* 3.2 3.5 + - - +
177A ALA* 2.8 29.2 + - + +
184A ILE* 4.6 5.8 - - + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 4.3 3.6 - - + -
164A LEU* 3.6 31.9 - - + -
169A GLN 3.7 2.8 + - - +
170A GLN 3.1 9.8 + - - +
171A ARG* 3.1 21.7 + - - +
173A ILE* 1.3 74.8 - - - +
175A ASP* 1.3 59.8 + - - +
177A ALA* 3.5 8.3 + - - +
178A ALA* 3.1 26.7 + - - +
184A ILE* 4.0 21.1 - - + +
227A PHE* 4.3 16.1 - - + -
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.7 34.6 + - - +
172A GLU* 3.6 7.4 - - - +
174A THR* 1.3 74.3 + - - +
176A TRP* 1.3 66.4 + - - +
178A ALA* 3.1 6.6 + - - +
179A ALA* 3.1 22.4 + - - +
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Residues in contact with TRP 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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143A VAL* 3.7 28.9 - - + -
146A LEU* 3.7 48.9 - - + -
147A GLU* 2.8 40.9 + - + +
150A VAL* 4.4 15.5 - - + -
156A VAL* 4.9 0.7 - - + -
157A PRO* 5.7 0.9 - - + -
172A GLU 2.9 18.4 + - - +
173A ILE 3.2 4.2 + - - +
175A ASP* 1.3 75.1 - - - +
177A ALA* 1.3 63.3 + - - +
179A ALA* 3.2 4.8 + - - +
180A HIS* 2.5 86.7 + + + -
182A VAL* 4.1 16.2 - - + -
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Residues in contact with ALA 177 (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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146A LEU* 6.2 0.9 - - + -
160A ASN* 5.8 0.7 - - + -
173A ILE* 2.8 17.5 + - + +
174A THR 3.6 6.3 - - - +
175A ASP 3.1 0.2 - - - -
176A TRP* 1.3 87.3 - - + +
178A ALA* 1.3 52.2 + - - +
180A HIS 3.1 1.0 + - - -
181A ASP 2.6 32.7 + - - -
182A VAL* 2.8 37.7 + - + +
184A ILE* 3.8 22.4 - - + -
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Residues in contact with ALA 178 (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 THR 3.1 17.7 + - - +
175A ASP* 3.1 7.4 + - - +
177A ALA* 1.3 75.3 - - - +
179A ALA* 1.3 60.2 + - - +
181A ASP* 3.4 20.4 + - - +
182A VAL 5.0 1.3 - - - -
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Residues in contact with ALA 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 ASP 3.1 12.1 + - - +
176A TRP* 3.5 11.0 - - - +
178A ALA* 1.3 77.1 - - - +
180A HIS* 1.3 75.1 + - + +
181A ASP* 3.9 5.6 + - - +
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Residues in contact with HIS 180 (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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9A ASN* 4.6 2.1 + - - -
147A GLU* 4.3 6.9 + - - -
150A VAL* 6.1 4.5 - - + -
156A VAL* 3.9 20.7 - - + +
176A TRP* 2.5 91.5 + + + +
177A ALA 4.0 1.1 - - - +
179A ALA* 1.3 88.4 - - + +
181A ASP* 1.3 73.4 + - - +
182A VAL* 3.2 5.1 + - + -
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Residues in contact with ASP 181 (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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9A ASN* 3.5 32.1 + - + +
177A ALA 2.6 11.8 + - - -
178A ALA* 3.4 16.0 + - - +
179A ALA 4.5 4.7 - - - +
180A HIS* 1.3 78.1 - - - +
182A VAL* 1.3 59.3 + - - +
183A LYS* 3.8 9.1 + - - +
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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