Contacts of the helix formed by residues 178 - 190 (chain A) in PDB entry 3H1J
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE* 5.1 0.7 - - - -
131A ARG* 5.2 0.2 - - - +
176A HIS 3.3 9.2 + - - -
177A LEU* 1.3 72.3 - - - +
179A ARG* 1.3 65.2 + - + +
180A ALA* 3.2 22.2 - - + +
181A ASP* 2.6 45.0 + - - +
182A LEU* 3.0 15.5 + - - +
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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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68A LYS* 5.4 8.1 - - - +
120A CYS 5.3 0.6 + - - -
121A ALA 3.5 18.6 + - - -
122A LEU* 3.2 31.2 + - + +
123A GLU* 5.4 0.2 - - - +
124A GLU* 4.1 30.8 - - + +
127A ILE* 3.6 31.3 - - + +
131A ARG* 5.7 0.2 - - - +
178A THR* 1.3 76.9 - - + +
180A ALA* 1.3 54.0 + - - +
182A LEU* 3.2 5.0 + - - +
183A ALA* 2.8 50.0 + - - +
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Residues in contact with ALA 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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178A THR* 3.2 15.8 - - + +
179A ARG* 1.3 83.1 - - - +
181A ASP* 1.3 59.0 + - - +
183A ALA* 2.9 9.8 - - - +
184A SER* 2.9 30.7 + - - -
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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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51A LYS 5.2 2.4 - - - +
52A ASN* 5.3 8.4 + - + +
55A ALA* 5.1 1.9 - - - +
176A HIS 5.0 0.5 - - - +
177A LEU* 3.6 28.2 - - + +
178A THR* 2.6 46.5 + - - +
180A ALA* 1.3 66.3 - - - +
182A LEU* 1.3 66.7 + - - +
184A SER* 3.1 9.4 + - - -
185A TYR* 2.9 24.0 + - - +
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Residues in contact with LEU 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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55A ALA* 4.6 4.0 - - - -
58A PHE* 3.9 28.3 - - + -
59A VAL* 3.9 18.5 - - + +
62A LEU* 3.9 28.0 - - + -
122A LEU* 4.5 9.2 - - + -
127A ILE* 3.9 18.2 - - + -
177A LEU* 4.0 34.5 - - + -
178A THR 3.4 14.8 - - - +
179A ARG 3.6 4.7 - - - +
181A ASP* 1.3 77.3 - - + +
183A ALA* 1.3 62.7 + - - +
185A TYR* 3.4 4.5 + - - +
186A ILE* 2.9 30.4 + - - +
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Residues in contact with ALA 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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122A LEU* 4.0 18.1 - - + +
179A ARG* 2.8 23.3 + - - +
180A ALA* 2.9 17.3 - - - +
182A LEU* 1.3 79.7 - - - +
184A SER* 1.3 63.7 + - - +
186A ILE* 3.1 12.4 + - - +
187A ASP* 2.8 22.0 + - - +
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Residues in contact with SER 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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180A ALA 2.9 15.6 + - - -
181A ASP* 3.1 12.6 + - - -
183A ALA* 1.3 69.5 - - - +
185A TYR* 1.3 67.4 + - - +
187A ASP* 2.9 11.6 + - - -
188A THR* 2.6 38.8 + - - -
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Residues in contact with TYR 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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43A ALA* 3.6 21.2 - - + +
44A GLY* 3.8 14.0 + - - -
47A TYR* 5.3 0.2 - - + -
48A GLU* 4.3 14.1 - - + -
52A ASN* 4.2 11.2 - - - +
55A ALA* 3.7 22.4 - - + -
56A GLY* 3.3 30.1 - - - -
59A VAL* 3.7 18.8 - - + -
95A THR* 4.3 4.9 + - - -
181A ASP 2.9 15.2 + - - +
182A LEU* 3.4 9.9 - - - +
184A SER* 1.3 79.2 + - - +
186A ILE* 1.3 66.6 + - - +
188A THR* 4.5 0.7 - - - -
189A HIS* 3.0 64.0 + + - +
190A PHE* 3.8 23.1 - + - -
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Residues in contact with ILE 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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59A VAL* 4.0 29.4 - - + -
117A VAL 3.8 13.9 - - - +
118A GLN 5.3 4.7 - - - +
120A CYS* 4.3 13.5 - - + +
122A LEU* 3.8 33.0 - - + -
182A LEU 2.9 16.8 - - - +
183A ALA 3.1 6.7 + - - +
185A TYR* 1.3 79.6 - - - +
187A ASP* 1.3 62.1 + - - +
190A PHE* 3.0 59.1 + - + +
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Residues in contact with ASP 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 ALA* 2.8 26.7 - - - +
184A SER* 2.9 10.3 + - - +
186A ILE* 1.3 78.9 - - - +
188A THR* 1.3 53.5 - - - +
190A PHE 4.8 0.7 - - - +
191A LYS* 2.7 38.9 - - - +
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Residues in contact with THR 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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184A SER* 2.6 35.9 + - - -
185A TYR* 3.9 2.2 - - - -
187A ASP* 1.3 75.5 - - - +
189A HIS* 1.3 76.3 + - + +
191A LYS* 3.7 18.5 + - - +
194A ARG* 3.0 18.1 + - - +
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Residues in contact with HIS 189 (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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41A ILE* 4.1 7.4 - - - +
43A ALA* 3.8 15.7 - - + -
47A TYR* 3.5 35.2 + + + +
52A ASN* 5.2 4.0 + - - -
185A TYR* 3.0 59.7 + + + +
188A THR* 1.3 93.3 - - + +
190A PHE* 1.3 57.5 + - + +
191A LYS* 2.5 21.3 + - - +
194A ARG* 2.8 46.3 + - - +
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Residues in contact with PHE 190 (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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41A ILE* 3.3 37.5 - - + -
43A ALA* 4.6 2.7 - - + -
56A GLY 5.8 1.3 - - - -
59A VAL* 4.0 28.5 - - + -
63A ALA* 6.0 1.6 - - + -
95A THR* 4.7 7.6 - - + -
97A PHE* 3.9 25.1 - + - -
116A VAL 5.8 0.4 - - - -
117A VAL* 3.8 25.4 - - - +
185A TYR* 3.8 25.8 - + - -
186A ILE* 3.0 41.2 + - + +
187A ASP* 4.8 0.3 - - - +
189A HIS* 1.3 69.9 - - + +
191A LYS* 1.3 62.4 + - - +
195A MET* 3.1 22.7 - - - +
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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