Contacts of the helix formed by residues 194 - 207 (chain A) in PDB entry 3IHL
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A VAL* 5.2 1.3 - - + -
192A GLN 5.2 0.9 - - - +
193A LYS* 1.3 73.0 - - - +
195A LYS* 1.3 66.6 + - - +
196A PRO* 3.3 2.9 - - - -
197A THR* 3.0 10.1 + - - +
198A GLN* 3.0 41.1 + - - +
226A VAL* 3.7 28.0 - - + +
229A LYS* 4.0 31.3 + - + +
230A ILE* 3.6 33.4 - - + -
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Residues in contact with LYS 195 (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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193A LYS* 5.6 2.0 - - + -
194A THR* 1.3 79.6 + - - +
196A PRO* 1.3 72.0 - - + +
198A GLN* 3.1 21.3 + - + +
199A ASN* 2.9 42.7 + - - +
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Residues in contact with PRO 196 (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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10A VAL* 3.6 26.3 - - + +
182A LEU 4.0 11.7 - - - +
184A PRO* 3.9 19.5 - - + -
193A LYS* 4.2 15.0 - - + +
194A THR 3.7 2.7 - - - -
195A LYS* 1.3 94.9 - - + +
197A THR* 1.3 57.5 + - - +
199A ASN* 3.5 7.3 + - + +
200A SER* 3.0 27.4 + - - -
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Residues in contact with THR 197 (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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181A SER* 2.7 31.1 + - - +
182A LEU 3.0 19.6 + - - -
183A VAL* 4.1 10.1 - - - +
194A THR* 3.0 10.5 + - - -
196A PRO* 1.3 76.0 - - - +
198A GLN* 1.3 61.2 + - - +
200A SER* 3.6 0.4 - - - -
201A VAL* 2.8 35.2 + - + +
214A ILE* 3.9 27.6 - - + -
216A CYS* 4.6 7.1 - - - -
230A ILE* 4.7 4.7 - - + -
234A CYS* 4.2 10.1 - - - -
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Residues in contact with GLN 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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194A THR* 3.0 35.6 + - - +
195A LYS* 3.1 24.1 + - + +
197A THR* 1.3 78.2 - - - +
199A ASN* 1.3 59.2 + - - +
201A VAL* 3.9 1.9 - - - +
202A ARG* 3.0 45.3 + - - +
229A LYS* 5.3 3.4 - - - +
230A ILE* 6.1 0.2 - - - -
233A PHE* 3.3 53.0 - - + +
234A CYS* 4.1 17.5 - - - +
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Residues in contact with ASN 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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195A LYS* 2.9 42.6 + - - +
196A PRO* 4.0 6.1 - - + +
198A GLN* 1.3 74.6 - - - +
200A SER* 1.3 61.3 + - - +
202A ARG* 3.5 22.5 + - - +
203A ALA* 3.0 28.4 + - - +
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Residues in contact with SER 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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9A GLY* 3.2 15.1 - - - -
10A VAL* 3.7 9.6 + - - -
151A ILE* 4.5 6.8 + - - +
179A HIS* 2.7 29.9 + - - -
181A SER* 3.9 9.0 - - - -
196A PRO 3.0 18.1 + - - -
197A THR 3.6 4.0 - - - -
199A ASN* 1.3 75.0 - - - +
201A VAL* 1.3 64.6 + - - +
203A ALA* 3.2 7.6 + - - +
204A LEU* 3.0 22.5 + - - +
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Residues in contact with VAL 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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179A HIS* 4.0 20.0 - - + -
197A THR* 2.8 26.7 + - + +
198A GLN 3.9 3.1 - - - +
200A SER* 1.3 77.0 - - - +
202A ARG* 1.3 58.4 + - - +
204A LEU* 3.2 8.7 + - - +
205A ARG* 3.0 58.5 + - - +
211A PRO* 4.1 13.0 - - + +
214A ILE* 3.9 26.2 - - + -
234A CYS* 4.2 15.9 - - + -
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Residues in contact with ARG 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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198A GLN* 3.0 35.0 + - - +
199A ASN* 3.7 23.7 + - - +
200A SER 3.2 0.2 - - - -
201A VAL* 1.3 80.2 - - - +
203A ALA* 1.3 57.3 + - - +
205A ARG* 3.4 9.5 - - - +
206A GLY* 2.8 24.8 + - - -
233A PHE 5.5 5.7 + - - -
235A HIS* 6.0 4.6 - - - -
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Residues in contact with ALA 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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151A ILE* 4.4 12.1 - - + +
152A GLY* 5.3 8.5 - - - -
199A ASN 3.0 18.9 + - - +
200A SER* 3.2 8.0 + - - +
202A ARG* 1.3 74.3 - - - +
204A LEU* 1.3 64.9 + - - +
206A GLY* 3.3 3.5 + - - +
207A LEU* 3.2 28.6 + - + +
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Residues in contact with LEU 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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7A THR* 4.2 5.8 - - + +
151A ILE* 3.7 37.4 - - + +
160A VAL* 4.7 4.5 - - + -
177A ASN* 3.9 20.0 - - - +
179A HIS* 3.8 30.3 - - + +
200A SER 3.0 13.0 + - - +
201A VAL* 3.2 8.3 + - - +
203A ALA* 1.3 74.6 - - - +
205A ARG* 1.3 65.0 + - - +
207A LEU* 3.1 13.7 + - - +
208A GLY 3.1 6.9 + - - -
209A LEU* 3.0 38.5 + - + +
211A PRO* 4.0 17.0 - - + -
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Residues in contact with ARG 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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201A VAL* 3.0 28.9 + - - +
202A ARG* 3.4 13.5 - - - +
204A LEU* 1.3 76.8 - - - +
206A GLY* 1.3 62.5 + - - +
208A GLY* 2.9 15.2 + - - -
209A LEU 3.1 9.5 + - - +
210A SER* 2.8 45.5 + - - +
211A PRO* 3.6 18.5 + - - +
234A CYS* 4.1 1.4 - - - +
235A HIS* 3.1 49.0 + - - +
236A VAL* 4.3 12.3 - - - +
202B ARG 5.0 3.1 - - - +
206B GLY* 3.1 45.1 + - - +
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Residues in contact with GLY 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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202A ARG 2.8 16.2 + - - -
203A ALA* 3.3 6.7 + - - -
204A LEU 3.2 0.4 - - - -
205A ARG* 1.3 78.3 - - - +
207A LEU* 1.3 59.9 + - - +
208A GLY 3.2 0.4 + - - -
202B ARG* 3.4 21.0 + - - +
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Residues in contact with LEU 207 (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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151A ILE* 4.0 21.3 - - + -
152A GLY* 4.5 4.3 - - - +
157A MET* 3.1 41.3 - - + -
160A VAL* 3.7 33.8 - - + +
161A GLU* 4.5 4.0 - - - +
164A ARG* 3.5 18.2 - - - +
203A ALA* 3.2 15.5 + - + +
204A LEU* 3.1 8.8 + - - +
206A GLY* 1.3 77.7 - - - +
208A GLY* 1.3 58.3 + - - +
209A LEU 3.6 0.4 - - - -
202B ARG* 4.1 12.9 + - - +
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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