Contacts of the helix formed by residues 176 - 188 (chain A) in PDB entry 1DIN
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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175A PRO* 1.3 70.8 - - - +
177A PRO* 1.3 71.0 - - + +
179A ARG* 3.2 12.7 + - - +
180A GLN* 3.0 20.6 + - - +
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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 PRO* 3.4 14.6 - - + +
176A ALA* 1.3 99.6 - - + +
178A SER* 1.3 62.7 + - - +
180A GLN* 3.2 12.1 + - + +
181A LEU* 3.1 28.0 + - + +
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Residues in contact with SER 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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150A GLU* 4.0 33.0 + - - +
174A VAL* 4.0 10.5 - - - -
175A PRO* 2.9 32.1 + - - +
177A PRO* 1.3 77.2 - - - +
179A ARG* 1.3 66.3 + - - +
181A LEU* 3.4 5.9 + - - +
182A ILE* 3.0 30.5 + - - +
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Residues in contact with ARG 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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169A GLY* 3.7 21.9 + - - -
174A VAL* 3.8 9.2 - - + +
175A PRO 3.1 7.9 + - - +
176A ALA* 3.3 14.4 - - - +
178A SER* 1.3 80.8 - - - +
180A GLN* 1.3 57.4 + - - +
182A ILE* 3.4 1.6 + - - +
183A THR* 2.9 37.4 + - - +
196A TRP* 3.6 58.7 - - + +
198A GLU* 2.7 43.6 + - - -
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Residues in contact with GLN 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 11.8 + - - +
177A PRO* 3.5 13.5 + - - +
178A SER 3.2 0.2 - - - -
179A ARG* 1.3 79.6 - - - +
181A LEU* 1.3 64.8 + - - +
183A THR* 3.3 4.8 + - - -
184A GLU* 2.8 67.2 + - + +
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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
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150A GLU* 4.2 23.8 - - + +
153A LEU* 3.7 23.0 - - + +
177A PRO* 3.1 16.4 + - + +
178A SER* 3.7 9.2 - - - +
180A GLN* 1.3 80.2 - - + +
182A ILE* 1.4 55.7 + - - +
184A GLU* 4.2 6.7 - - - +
185A GLY* 2.8 31.7 + - - -
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Residues in contact with ILE 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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149A LEU* 4.2 17.0 - - + +
150A GLU* 3.9 36.1 - - - +
153A LEU* 4.5 7.4 - - + -
167A MET* 4.4 11.7 - - + -
174A VAL* 4.1 21.8 - - + -
178A SER 3.0 22.5 + - - +
179A ARG 3.8 2.9 - - - +
181A LEU* 1.4 73.0 - - - +
183A THR* 1.3 59.8 + - - +
186A PHE* 2.7 57.8 + - + +
194A VAL* 4.6 8.7 - - + -
196A TRP* 4.1 15.9 - - + -
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Residues in contact with THR 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 ARG* 2.9 25.4 + - - +
180A GLN* 3.7 6.7 - - - -
182A ILE* 1.3 78.8 - - - +
184A GLU* 1.3 67.7 + - + +
186A PHE* 4.3 1.6 - - - +
187A GLY* 3.0 22.2 + - - -
194A VAL* 6.0 2.9 - - - -
196A TRP* 3.4 28.0 + - + +
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLN* 2.8 53.3 + - + +
181A LEU* 4.2 6.3 - - - +
183A THR* 1.3 81.1 - - + +
185A GLY* 1.3 64.5 - - - +
187A GLY* 3.3 12.0 + - - -
188A ALA* 3.7 6.6 + - - +
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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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153A LEU* 4.5 12.6 - - - -
156A VAL* 3.6 14.7 - - - +
181A LEU 2.8 19.2 + - - -
184A GLU* 1.3 75.1 - - - +
186A PHE* 1.3 66.9 + - - +
187A GLY 3.2 0.5 + - - -
188A ALA* 3.3 17.8 + - - +
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Residues in contact with PHE 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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130A PHE* 3.6 25.4 - + - -
149A LEU* 4.2 24.7 - - + -
153A LEU* 3.5 24.7 - - + -
156A VAL* 3.8 16.2 - - + -
165A PHE* 3.8 29.8 - + + -
182A ILE* 2.7 32.3 + - + +
183A THR 4.5 0.9 - - - +
185A GLY* 1.3 72.8 - - - -
187A GLY* 1.3 60.6 + - - +
188A ALA 3.1 2.5 + - - -
189A ASN* 3.2 21.8 + - - +
192A LEU* 3.8 29.4 - - + +
194A VAL* 3.3 33.0 - - + -
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Residues in contact with GLY 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 THR 3.0 19.5 + - - -
184A GLU* 3.6 4.7 - - - -
185A GLY 3.1 0.8 - - - -
186A PHE* 1.3 77.5 - - - +
188A ALA* 1.3 58.7 + - - +
189A ASN 3.3 3.8 + - - -
190A PRO* 4.9 1.6 - - - +
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Residues in contact with ALA 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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156A VAL* 4.9 4.7 - - + -
184A GLU 3.7 6.1 + - - +
185A GLY* 3.3 14.3 + - - +
186A PHE 3.1 0.6 - - - -
187A GLY* 1.3 80.5 - - - +
189A ASN* 1.3 57.6 + - - +
190A PRO* 3.7 8.6 - - - +
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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