Contacts of the helix formed by residues 176 - 186 (chain A) in PDB entry 3A7E
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 ALA 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 4.4 13.5 - - + +
147A TYR* 3.9 35.7 - - + -
170A ASN 3.9 3.3 + - - +
171A VAL* 4.0 16.8 + - + -
175A GLY* 1.3 73.9 - - - +
177A PRO* 1.3 57.2 - - - +
178A ASP* 3.4 3.4 - - - +
179A PHE* 3.2 12.0 + - + -
180A LEU* 2.8 34.3 + - - +
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Residues in contact with PRO 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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175A GLY* 3.4 10.1 - - - +
176A ALA* 1.3 90.0 - - - +
178A ASP* 1.3 60.3 + - + +
180A LEU* 3.8 8.3 - - + +
181A ALA* 2.9 30.5 + - - +
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Residues in contact with ASP 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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144A LYS 4.6 9.5 - - - +
145A ASP* 4.7 7.4 - - - +
148A LEU* 3.9 31.8 + - + +
149A PRO* 4.7 5.5 - - - +
176A ALA* 4.3 4.2 - - - +
177A PRO* 1.3 80.0 - - + +
179A PHE* 1.3 81.0 + - - +
181A ALA* 3.5 5.9 + - - +
182A HIS* 3.0 28.4 + - - +
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Residues in contact with PHE 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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140A LEU* 4.5 13.7 - - + -
147A TYR* 3.7 32.8 - + + -
148A LEU* 4.0 22.0 - - + +
151A THR* 3.4 33.7 - - + -
166A LEU* 4.6 9.6 - - + -
168A ALA* 3.5 30.5 - - + -
171A VAL* 4.7 6.1 - - + -
176A ALA* 3.2 11.2 + - + +
178A ASP* 1.3 83.2 + - - +
180A LEU* 1.3 69.9 + - - +
182A HIS* 3.1 3.6 + + + -
183A VAL* 3.0 51.1 + - + +
189A PHE* 6.2 0.4 - + - -
208A GLU* 5.3 4.3 - - + -
210A ALA* 5.0 4.9 - - + -
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Residues in contact with LEU 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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171A VAL* 3.4 44.6 - - + +
172A ILE* 5.2 3.8 - - + -
176A ALA 2.8 19.7 + - - +
177A PRO* 3.8 7.9 - - + +
179A PHE* 1.3 74.4 - - + +
181A ALA* 1.3 62.3 + - - +
183A VAL* 3.8 4.9 - - + -
184A ARG* 3.1 73.0 + - + +
208A GLU* 3.8 26.7 - - + +
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Residues in contact with ALA 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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177A PRO 2.9 20.3 + - - +
178A ASP* 3.7 7.4 - - - +
179A PHE 3.2 0.2 - - - -
180A LEU* 1.3 76.9 - - - +
182A HIS* 1.3 61.2 + - - +
184A ARG* 4.5 2.0 - - - +
185A GLY* 3.3 19.9 + - - -
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Residues in contact with HIS 182 (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 LEU* 3.9 29.0 - - + +
151A THR* 5.4 5.3 - - + +
152A LEU* 4.0 24.4 - - + +
155A GLU* 5.4 2.0 + - - -
178A ASP 3.0 17.4 + - - +
179A PHE* 3.1 5.3 + + + +
181A ALA* 1.3 76.4 - - - +
183A VAL* 1.3 60.5 + - + +
185A GLY 3.8 0.2 - - - -
186A SER* 2.9 47.1 + - - -
189A PHE* 4.3 20.5 - + - -
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Residues in contact with VAL 183 (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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179A PHE* 3.0 42.3 + - + +
180A LEU* 3.5 18.2 - - + +
182A HIS* 1.3 76.3 - - + +
184A ARG* 1.3 69.8 + - - +
186A SER 3.5 8.8 + - - +
189A PHE* 3.2 38.5 - - + +
191A CYS* 3.0 27.8 - - - -
208A GLU* 5.0 2.7 - - + -
210A ALA* 3.0 24.5 - - + -
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Residues in contact with ARG 184 (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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172A ILE* 5.8 1.6 - - - +
180A LEU* 3.1 48.2 + - + +
181A ALA* 4.5 2.2 - - - +
183A VAL* 1.3 77.3 - - - +
185A GLY* 1.3 59.7 + - - +
186A SER 3.8 2.8 + - - +
189A PHE 5.0 1.7 - - - +
191A CYS* 4.0 13.2 - - + -
193A HIS* 3.9 20.6 + - - +
208A GLU* 3.0 39.1 + - - +
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Residues in contact with GLY 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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181A ALA 3.3 16.1 + - - -
184A ARG* 1.3 77.4 - - - +
186A SER* 1.3 65.0 + - - +
187A SER* 3.7 1.4 + - - -
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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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182A HIS* 2.9 34.6 + - - -
183A VAL 3.6 2.1 - - - +
184A ARG 3.5 2.7 - - - +
185A GLY* 1.3 78.8 - - - +
187A SER* 1.3 60.3 + - - +
188A CYS* 3.1 25.1 + - - +
189A PHE* 3.2 40.1 - - - +
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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