Contacts of the helix formed by residues 177 - 188 (chain C) in PDB entry 1H88
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 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C HIS 3.2 27.6 - - - +
136C ASN* 3.3 23.7 + - - +
142C VAL* 4.0 23.7 - - + +
170C ALA* 4.3 1.3 - - - -
175C GLY 5.9 0.2 - - - -
176C ARG* 1.3 76.3 - - - +
178C ASP* 1.3 67.7 + - - +
179C ASN* 3.1 5.0 + - - +
180C ALA* 3.1 28.9 + - + +
181C ILE* 3.2 11.4 + - - +
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASN* 5.1 2.6 + - - -
166C TRP* 3.6 25.2 - - + +
167C ALA* 3.6 20.6 - - - +
170C ALA* 4.0 11.8 - - + +
176C ARG 4.0 0.6 + - - -
177C THR* 1.3 75.3 - - - +
179C ASN* 1.3 58.9 + - - +
181C ILE* 3.8 3.4 - - - +
182C LYS* 2.7 40.3 + - - +
6E C 4.4 19.5 + - - +
7E C 4.2 19.8 + - - -
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Residues in contact with ASN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLU* 5.5 1.3 - - - -
136C ASN* 3.4 28.9 + - - +
137C HIS* 5.2 3.0 - - - -
177C THR* 3.0 5.2 + - - +
178C ASP* 1.3 85.2 - - - +
180C ALA* 1.3 60.3 + - - +
182C LYS* 3.6 14.2 + - - +
183C ASN* 2.9 35.5 + - - +
18D A 3.6 20.6 + - - -
19D A 3.2 46.1 + - - +
20D C 5.6 0.3 + - - -
8E G 5.0 0.5 - - - +
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 6.5 0.9 - - + -
147C TRP* 4.1 19.5 - - + -
176C ARG* 4.9 4.5 - - + -
177C THR* 3.1 23.3 + - + +
179C ASN* 1.3 78.2 - - - +
181C ILE* 1.3 55.7 + - - +
183C ASN* 2.9 8.8 + - - +
184C HIS* 2.7 34.1 + - - +
18D A 5.7 3.6 - - - -
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TRP* 4.0 14.8 - - + -
155C ILE* 4.1 22.1 - - + +
166C TRP* 4.1 15.5 - - + +
169C ILE* 4.0 23.6 - - + -
170C ALA* 3.4 43.5 - - + +
173C LEU* 4.1 9.0 - - + -
176C ARG* 3.9 20.9 - - + -
177C THR 3.2 8.5 + - - +
178C ASP* 3.8 5.4 - - - +
180C ALA* 1.3 75.7 - - - +
182C LYS* 1.3 66.7 + - - +
184C HIS* 3.2 3.0 + - - +
185C TRP* 3.1 23.0 + - - +
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TRP* 3.1 46.8 - - + +
178C ASP* 2.7 25.2 + - - +
179C ASN* 3.6 14.8 + - - +
181C ILE* 1.3 72.8 - - - +
183C ASN* 1.3 66.8 + - - +
185C TRP* 3.7 1.7 - - - +
186C ASN* 3.1 47.2 + - - +
19D A 3.2 15.6 - - - +
7E C 4.4 9.6 - - - -
8E G 3.1 34.9 + - - +
9E T 2.6 31.0 + - + +
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Residues in contact with ASN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 2.9 27.0 + - - +
180C ALA* 3.4 4.9 - - - +
182C LYS* 1.3 75.5 - - - +
184C HIS* 1.3 71.5 + - - +
186C ASN* 3.0 19.4 + - - +
187C SER* 3.4 9.0 + - - -
17D T 3.3 43.1 - - + +
18D A 2.9 52.4 + - - -
19D A 4.4 2.6 + - - -
9E T 4.5 3.6 - - - +
10E T 4.9 0.2 - - - +
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TRP* 3.1 64.3 + + + +
152C ASP* 3.0 27.3 + - - -
155C ILE* 4.5 4.5 - - + -
180C ALA 2.7 15.5 + - - +
181C ILE* 3.4 13.9 - - - +
183C ASN* 1.3 72.6 - - - +
185C TRP* 1.3 58.1 + - - +
187C SER* 4.8 0.2 - - - -
188C THR* 2.8 53.3 + - + +
189C MET* 4.3 13.5 - - + -
17D T 5.5 7.2 + - - -
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Residues in contact with TRP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ILE* 3.7 9.4 - - + -
156C TYR* 3.7 36.8 - + - -
159C HIS* 3.2 58.4 + + + -
160C LYS* 5.1 0.9 - - + -
164C ASN* 6.1 0.4 - - - -
166C TRP* 4.0 15.3 - + + -
181C ILE 3.1 12.0 + - - +
182C LYS 3.7 3.6 - - - +
184C HIS* 1.3 78.6 - - - +
186C ASN* 1.3 81.6 + - - +
187C SER 2.8 2.8 + - - -
189C MET* 2.9 75.4 + - + +
190C ARG 5.3 2.9 + - - -
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Residues in contact with ASN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ASN* 5.4 1.6 - - - +
166C TRP* 4.3 13.5 - - - -
182C LYS* 3.1 24.0 + - - +
183C ASN* 3.0 18.0 + - - +
185C TRP* 1.3 89.6 - - - +
187C SER* 1.3 57.9 + - - +
190C ARG* 3.6 17.5 - - - +
17D T 4.6 9.2 - - + -
9E T 3.5 27.0 - - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN 3.4 4.9 + - - -
184C HIS 4.8 0.4 - - - -
185C TRP 2.8 0.6 + - - -
186C ASN* 1.3 79.0 + - - +
188C THR* 1.3 68.0 + - - +
190C ARG* 3.9 7.9 + - - +
15D C 4.9 0.3 - - - +
16D T 3.2 54.8 + - - +
17D T 4.1 15.5 - - - +
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Residues in contact with THR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASP* 4.3 4.0 - - - +
184C HIS* 2.8 46.1 + - + +
187C SER* 1.3 77.2 - - - +
189C MET* 1.3 73.4 + - + +
190C ARG* 2.6 20.6 + - - +
16D T 5.6 2.4 + - - -
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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