Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 3INH
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 PRO 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 3.6 25.4 - - - +
100A PHE 6.0 0.7 - - - +
182A GLY 4.6 2.7 - - - +
183A LEU* 6.2 0.2 - - - -
184A ALA 3.9 10.3 - - - +
185A TYR 4.1 2.9 - - - -
186A ALA* 3.6 38.8 - - + +
189A ALA* 4.8 0.2 - - + -
195A LEU 3.4 7.0 - - - +
196A GLU* 1.3 90.8 - - + +
198A PHE* 1.3 67.3 + - - +
199A PHE* 4.6 2.9 - - + +
200A ASP* 3.2 29.6 + - - +
201A SER* 3.2 17.5 + - - -
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Residues in contact with PHE 198 (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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80A MET* 4.2 11.2 - - + -
98A SER 4.8 0.8 + - - -
100A PHE* 4.5 19.4 - + + +
147A VAL* 3.7 22.7 - - + -
148A SER* 6.2 0.2 - - - -
149A ILE* 4.2 22.9 - - + -
157A VAL* 3.6 28.7 - - + -
159A ALA* 3.6 22.7 - - + -
160A ASN 5.9 1.3 + - - +
181A LEU* 3.6 37.2 - - + -
182A GLY 4.7 7.0 + - - +
183A LEU* 4.9 3.1 - - + -
196A GLU 3.9 0.4 + - - -
197A PRO* 1.3 71.3 - - - +
199A PHE* 1.3 67.2 + + + +
201A SER* 3.0 10.6 + - - -
202A LEU* 2.9 46.0 + - + -
238A ILE* 5.4 1.6 - - + -
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Residues in contact with PHE 199 (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 GLY 5.3 1.4 + - - -
183A LEU* 4.0 30.0 - - + +
184A ALA 6.1 0.2 - - - +
197A PRO* 3.4 2.5 - - + +
198A PHE* 1.3 86.1 - + - +
200A ASP* 1.3 56.9 + - - +
202A LEU* 3.3 14.6 + - + +
203A VAL* 3.0 39.3 + - + +
208A VAL* 5.1 0.4 - - + -
209A PRO 4.3 2.5 - - - -
210A ASN* 3.5 16.2 - - - -
211A LEU 3.5 33.0 - - - -
212A PHE* 3.8 17.0 - + + -
238A ILE* 3.8 30.3 - - + -
409A ARG* 3.4 34.8 - - - +
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Residues in contact with ASP 200 (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 ALA 4.7 1.4 - - - +
185A TYR* 5.1 3.5 - - - -
186A ALA* 4.8 5.0 + - - -
196A GLU* 3.7 17.9 - - + +
197A PRO* 3.2 36.7 + - - +
198A PHE 3.2 0.6 - - - -
199A PHE* 1.3 74.6 - - - +
201A SER* 1.3 65.2 + - - +
203A VAL* 3.9 3.3 - - - +
204A LYS* 3.0 39.8 + - - +
409A ARG* 3.2 26.4 + - - +
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Residues in contact with SER 201 (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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157A VAL* 4.9 2.5 - - - -
158A ARG 4.0 10.0 + - - -
159A ALA* 4.5 11.0 - - - -
160A ASN* 4.9 1.7 + - - -
196A GLU* 2.6 37.3 + - - +
197A PRO 3.2 5.0 + - - -
198A PHE* 3.0 11.7 + - - -
200A ASP* 1.3 77.8 - - - +
202A LEU* 1.3 57.8 + - - +
204A LYS* 3.4 1.7 + - - -
205A GLN* 2.9 53.8 + - - +
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Residues in contact with LEU 202 (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 ILE* 6.4 0.2 - - + -
153A PRO* 4.6 5.2 - - + -
155A VAL* 3.7 29.4 - - + -
157A VAL* 3.8 21.3 - - + +
198A PHE* 2.9 31.6 + - + +
199A PHE* 3.5 29.2 - - + +
200A ASP 3.2 0.2 - - - -
201A SER* 1.3 76.6 - - - +
203A VAL* 1.3 58.5 + - - +
206A THR* 2.6 41.6 + - - +
208A VAL* 4.4 9.4 - - + -
238A ILE* 3.8 32.8 - - + -
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Residues in contact with VAL 203 (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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199A PHE* 3.0 46.5 + - + +
200A ASP* 4.0 4.7 - - - +
202A LEU* 1.3 77.4 - - + +
204A LYS* 1.3 62.0 + - + +
206A THR* 2.7 24.5 - - - +
208A VAL* 3.9 20.4 - - + +
209A PRO 4.3 0.9 - - - +
210A ASN* 3.6 32.8 - - + +
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Residues in contact with LYS 204 (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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196A GLU* 3.0 30.3 + - - +
200A ASP* 3.0 28.4 + - - +
201A SER* 4.0 3.6 - - - +
203A VAL* 1.3 82.4 - - + +
205A GLN* 1.3 63.7 + - + +
206A THR 4.3 1.2 - - - +
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Residues in contact with GLN 205 (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 THR 4.8 1.0 - - - +
157A VAL* 3.4 16.1 - - + -
158A ARG* 2.8 52.1 + - - +
196A GLU* 4.7 3.8 + - - -
201A SER* 2.9 29.9 + - - +
204A LYS* 1.3 80.6 - - + +
206A THR* 1.3 62.6 + - + +
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Residues in contact with THR 206 (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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155A VAL* 3.8 28.3 - - + -
156A THR 4.7 3.4 - - - +
157A VAL* 3.6 23.1 - - + -
202A LEU* 2.6 22.8 + - + +
203A VAL 2.7 18.0 - - - +
204A LYS 4.3 1.7 - - - +
205A GLN* 1.3 83.5 - - + +
207A HIS* 1.3 65.9 + - - +
208A VAL* 3.2 28.4 + - - +
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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