Contacts of the helix formed by residues 178 - 190 (chain N) in PDB entry 3H1I
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124N GLU* 5.9 1.3 - - - +
127N ILE* 5.2 0.7 - - - -
131N ARG* 5.4 0.4 - - - +
176N HIS 3.1 10.1 + - - -
177N LEU* 1.3 73.2 - - - +
179N ARG* 1.3 83.2 - - + +
180N ALA* 2.7 16.8 + - + +
181N ASP* 2.9 34.6 + - - +
182N LEU* 3.1 14.4 - - - +
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Residues in contact with ARG 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N LYS* 5.3 9.1 - - - +
121N ALA 3.8 19.8 + - - -
122N LEU* 3.5 31.2 + - + +
123N GLU* 5.8 0.2 - - - +
124N GLU* 4.3 32.0 + - + +
127N ILE* 3.9 26.1 - - + +
131N ARG* 6.0 0.2 - - - +
178N THR* 1.3 76.9 - - + +
180N ALA* 1.3 63.9 + - - +
182N LEU* 3.5 4.4 + - - +
183N ALA* 3.0 31.8 + - - +
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Residues in contact with ALA 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N THR* 2.7 10.5 + - + +
179N ARG* 1.3 80.7 - - - +
181N ASP* 1.3 58.3 + - - +
183N ALA* 2.4 34.7 + - - +
184N SER* 2.7 17.4 + - - -
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Residues in contact with ASP 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N LYS* 5.3 4.2 - - - +
52N ASN* 5.5 11.2 + - + +
55N ALA* 4.8 3.0 - - - +
177N LEU* 3.7 24.0 - - + +
178N THR* 2.9 34.9 + - - +
180N ALA* 1.3 74.5 - - - +
182N LEU* 1.3 57.3 + - - +
184N SER* 2.4 25.8 + - - -
185N TYR* 3.0 12.1 + - - +
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Residues in contact with LEU 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N ALA* 4.9 4.3 - - + -
58N PHE* 4.0 34.1 - - + +
59N VAL* 4.1 14.4 - - + -
62N LEU* 4.6 5.6 - - + -
122N LEU* 5.2 9.4 - - + -
127N ILE* 4.0 24.0 - - + -
177N LEU* 3.8 37.5 - - + +
178N THR 3.1 21.5 - - - +
179N ARG* 3.8 6.1 - - - +
180N ALA 2.8 1.2 + - - -
181N ASP* 1.3 73.9 - - - +
183N ALA* 1.3 71.5 + - - +
185N TYR* 3.0 8.2 + - - +
186N ILE* 3.0 27.5 + - - +
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Residues in contact with ALA 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N LEU* 4.0 20.4 - - + +
179N ARG* 3.0 24.4 + - - +
180N ALA* 2.4 23.6 + - - +
182N LEU* 1.3 74.9 - - - +
184N SER* 1.3 59.2 + - - +
186N ILE* 3.1 13.0 + - - +
187N ASP* 3.2 21.2 + - - +
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Residues in contact with SER 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N ASN* 6.0 0.2 + - - -
180N ALA 2.7 12.6 + - - -
181N ASP* 2.4 33.1 + - - -
183N ALA* 1.3 71.4 - - - +
185N TYR* 1.3 59.7 + - - +
187N ASP* 3.0 8.8 + - - +
188N THR* 2.6 47.3 + - - -
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Residues in contact with TYR 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N ALA* 3.6 8.8 - - + +
44N GLY* 3.4 38.3 + - - -
48N GLU* 4.3 5.8 - - + -
52N ASN* 4.3 12.3 - - - +
55N ALA* 3.4 24.0 - - + -
56N GLY* 3.2 35.2 - - - -
59N VAL* 4.2 12.3 - - + -
95N THR* 4.0 4.0 + - - -
181N ASP 3.0 9.7 + - - +
182N LEU* 3.0 8.5 + - - +
184N SER* 1.3 80.9 + - - +
186N ILE* 1.3 62.0 + - - +
188N THR* 4.4 1.1 - - - -
189N HIS* 2.8 65.2 + + + +
190N PHE* 3.5 27.4 - + - -
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Residues in contact with ILE 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N VAL* 4.0 21.1 - - + -
116N VAL 5.5 0.2 - - - +
117N VAL 3.5 15.3 - - - +
118N GLN 4.6 8.3 - - - +
120N CYS* 4.2 13.9 - - + -
122N LEU* 3.8 38.4 - - + -
182N LEU 3.0 15.9 + - - +
183N ALA* 3.3 5.8 - - - +
185N TYR* 1.3 76.6 - - - +
187N ASP* 1.3 58.9 + - - +
190N PHE* 2.6 68.4 + - + +
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Residues in contact with ASP 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N ALA* 3.2 19.0 + - - +
184N SER* 3.0 9.1 + - - +
186N ILE* 1.3 78.7 - - - +
188N THR* 1.3 69.5 + - - +
189N HIS 3.2 0.9 + - - -
190N PHE 5.2 0.7 - - - -
191N LYS* 3.0 30.7 - - - +
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Residues in contact with THR 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N SER* 2.6 37.9 + - - -
185N TYR* 4.0 2.2 - - - -
187N ASP* 1.3 76.3 - - - +
189N HIS* 1.3 78.2 + - + +
191N LYS* 4.2 12.3 + - - +
194N ARG* 3.5 13.7 + - - -
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Residues in contact with HIS 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N ILE* 4.5 4.5 - - - +
43N ALA* 4.0 15.5 - - + -
47N TYR* 3.6 36.0 + + + +
52N ASN* 4.5 8.1 + - - -
185N TYR* 2.8 60.1 + + + +
187N ASP 4.2 0.2 - - - -
188N THR* 1.3 93.2 - - + +
190N PHE* 1.3 57.5 + - + +
191N LYS* 2.7 18.3 + - - +
194N ARG* 3.0 48.4 + - - +
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Residues in contact with PHE 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N ILE* 3.4 36.8 - - + -
43N ALA* 4.0 11.4 - - + -
56N GLY 5.7 0.2 - - - -
59N VAL* 3.6 32.8 - - + -
63N ALA* 6.2 0.4 - - + -
95N THR* 5.0 6.1 - - + -
97N PHE* 4.2 14.1 - + - -
116N VAL 5.5 1.8 - - - -
117N VAL* 3.5 21.8 - - - +
185N TYR* 3.5 25.6 - + - -
186N ILE* 2.6 48.5 + - + +
187N ASP* 4.4 1.0 - - - +
189N HIS* 1.3 68.1 - - - +
191N LYS* 1.3 61.6 + - - +
195N MET* 3.2 22.2 - - + +
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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