Contacts of the helix formed by residues 171 - 180 (chain A) in PDB entry 6MOL
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A HIS* 3.5 4.3 - - - -
162A VAL 4.9 3.1 - - - -
163A ASN* 4.7 11.4 - - + +
164A ALA 3.4 11.2 - - - +
165A VAL* 4.4 11.7 - - + -
169A GLY 4.4 6.3 - - - +
170A GLY* 1.3 75.8 - - - -
172A PRO* 1.3 69.7 - - - +
173A LEU* 3.7 10.0 + - - +
174A HIS* 2.8 48.6 + - - +
175A GLU* 3.3 8.1 + - - +
194A ASP* 5.1 1.2 + - + -
197A ALA* 3.8 24.6 - - + +
205A PRO* 4.8 0.2 - - - +
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Residues in contact with PRO 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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140A LEU* 3.9 35.4 - - + +
141A HIS* 3.3 29.4 - - + +
144A ALA* 3.5 18.6 - - + +
161A ASP 4.2 5.2 - - - +
162A VAL 3.6 19.7 - - - +
164A ALA* 3.4 9.9 - - + +
171A THR* 1.3 87.3 - - - +
173A LEU* 1.3 59.4 + - - +
175A GLU* 3.4 1.8 + - + +
176A ALA* 3.2 20.4 + - - +
188A LEU* 3.7 15.2 - - + +
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Residues in contact with LEU 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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162A VAL 5.1 1.6 + - - +
171A THR* 3.1 10.2 + - - +
172A PRO* 1.3 76.4 - - - +
174A HIS* 1.3 60.0 + - - +
176A ALA* 4.5 0.4 - - - +
177A ALA* 3.0 32.1 + - + +
185A VAL* 3.8 42.8 - - + +
188A LEU* 4.0 17.8 - - + +
189A LEU* 3.9 16.4 - - + -
193A ALA* 4.2 11.4 - - + -
194A ASP 3.8 21.5 - - - +
195A VAL* 3.8 15.7 - - - -
205A PRO* 3.9 16.4 - - + -
221A LEU* 4.1 9.6 - - + -
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Residues in contact with HIS 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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169A GLY 4.8 1.3 - - - -
170A GLY* 4.1 6.8 - - - -
171A THR* 2.8 37.7 + - - +
173A LEU* 1.3 76.8 - - - +
175A GLU* 1.3 61.1 + - + +
177A ALA* 3.4 2.6 + - - +
178A ARG* 2.9 41.9 + - - +
197A ALA* 3.2 32.5 - - + -
198A VAL 4.2 1.8 - - - -
199A ASP* 3.5 20.4 + - + -
203A GLY 2.8 22.5 + - - -
204A THR 3.3 12.9 - - - -
205A PRO* 3.6 21.1 - - + -
208A GLU* 4.0 14.5 - - + +
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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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141A HIS* 4.2 25.0 - - + +
144A ALA* 3.9 5.9 - - + +
145A ARG* 3.6 33.6 - - - +
166A ASP* 4.8 8.1 - - - +
170A GLY* 5.7 2.5 - - - -
171A THR 3.3 9.7 + - - +
172A PRO 3.4 5.6 + - - +
174A HIS* 1.3 77.6 - - + +
176A ALA* 1.3 57.4 + - - +
178A ARG* 2.9 32.2 + - - +
179A ALA* 3.0 30.8 + - - +
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Residues in contact with ALA 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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144A ALA* 4.0 8.0 + - + -
172A PRO 3.2 16.8 + - - +
173A LEU 4.0 2.5 - - - +
174A HIS 3.3 0.2 - - - -
175A GLU* 1.3 77.2 - - - +
177A ALA* 1.3 57.3 + - - +
179A ALA* 4.8 1.3 - - - -
180A GLY* 3.0 24.3 + - - -
181A HIS* 3.4 9.6 + - - -
184A ILE* 3.7 27.8 - - + -
185A VAL* 3.6 22.0 - - + -
188A LEU* 4.3 7.2 - - + -
217A ILE* 3.8 1.6 - - - +
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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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173A LEU* 3.0 20.2 + - + +
174A HIS 4.1 2.5 - - - +
176A ALA* 1.3 76.5 - - - +
178A ARG* 1.3 60.1 + - - +
185A VAL* 4.2 2.4 - - + +
205A PRO* 3.6 32.3 - - + +
208A GLU* 3.9 1.1 - - + +
209A ALA* 3.5 19.2 - - + +
214A HIS* 3.4 20.6 - - - -
217A ILE* 4.2 19.0 - - + +
221A LEU* 4.5 2.2 - - + -
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Residues in contact with ARG 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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170A GLY* 6.2 1.6 - - - -
174A HIS* 2.9 25.2 + - - +
175A GLU* 2.9 41.7 + - - +
177A ALA* 1.3 76.5 - - - +
179A ALA* 1.3 63.9 + - - +
199A ASP* 5.6 3.2 + - - -
208A GLU* 3.3 45.2 + - + +
212A ALA* 3.9 10.1 - - + +
214A HIS* 3.7 7.4 + - - -
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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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145A ARG* 4.1 13.5 - - - +
175A GLU 3.0 18.6 + - - +
178A ARG* 1.3 79.1 - - - +
180A GLY* 1.3 59.2 + - - +
181A HIS* 3.5 27.4 - - + +
214A HIS* 3.0 15.8 + - - -
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Residues in contact with GLY 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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176A ALA 3.0 8.2 + - - -
178A ARG 3.7 0.4 - - - -
179A ALA* 1.3 78.9 - - - +
181A HIS* 1.3 70.4 + - - +
182A LEU 3.9 1.4 + - - -
214A HIS* 3.4 28.2 + - - -
217A ILE* 3.7 7.6 - - - -
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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