Contacts of the helix formed by residues 192 - 201 (chain A) in PDB entry 1YYH
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A HIS* 3.7 2.7 - - - -
183A LYS 4.7 2.0 - - - -
184A ASP* 3.6 24.7 - - - +
185A MET 3.3 3.4 - - - +
186A GLN* 4.0 2.9 - - + -
190A GLU 3.8 0.6 + - - -
191A GLU* 1.3 75.0 - - - +
193A PRO* 1.4 75.3 - - - +
194A LEU* 3.6 9.3 + - - +
195A PHE* 3.1 24.6 + - - +
196A LEU* 3.1 21.1 + - - +
215A ASN 4.9 4.3 + - - +
218A ILE* 3.5 44.5 + - + -
226A PRO* 4.7 2.1 - - - +
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Residues in contact with PRO 193 (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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159A SER* 4.7 0.4 - - - +
161A LEU* 3.9 40.6 - - + +
162A HIS* 3.6 26.9 - - + +
165A ALA* 3.1 13.3 - - + +
182A ASN 4.6 2.5 - - - +
183A LYS 3.5 18.8 - - - +
185A MET 3.3 15.3 - - - +
192A THR* 1.4 84.7 - - - +
194A LEU* 1.3 57.1 + - - +
196A LEU* 3.2 2.7 + - + +
197A ALA* 2.9 25.1 + - - +
209A LEU* 3.8 16.4 - - + -
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Residues in contact with LEU 194 (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 LYS 5.1 0.6 + - - -
192A THR* 3.2 8.8 + - - +
193A PRO* 1.3 78.2 - - - +
195A PHE* 1.3 63.8 + - - +
197A ALA* 3.3 1.2 + - - +
198A ALA* 2.9 25.0 + - + +
206A ALA* 4.0 37.0 - - + +
209A LEU* 3.6 15.0 - - + +
210A LEU* 3.8 21.1 - - + -
214A ALA* 4.5 15.7 - - + +
215A ASN 4.1 5.8 - - - +
216A ARG* 3.7 38.6 - - + +
226A PRO* 4.0 13.0 - - + -
238A ILE* 6.3 0.2 - - + -
242A LEU* 4.3 8.5 - - + -
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Residues in contact with PHE 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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189A ARG* 5.5 0.4 - - - -
191A GLU* 3.6 36.8 - - + -
192A THR* 3.1 29.7 + - - +
194A LEU* 1.3 77.9 - - - +
196A LEU* 1.3 61.5 + - + +
198A ALA* 3.3 2.4 + - - +
199A ARG* 2.8 33.3 + - + -
218A ILE 5.0 2.5 - - - +
220A ASP* 3.3 30.5 - - + -
224A ARG* 3.3 29.6 - - + -
225A LEU 3.8 2.5 - - - -
226A PRO* 3.9 24.0 - - + +
229A ILE* 3.5 44.4 - - + +
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Residues in contact with LEU 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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158A LYS* 4.1 23.3 - - + +
162A HIS* 3.7 52.3 - - + +
165A ALA 4.6 1.1 - - - -
166A ALA* 4.4 14.8 - - + +
187A ASN* 4.4 0.9 - - - +
189A ARG* 6.0 0.4 - - - +
191A GLU* 3.4 33.4 - - + +
192A THR 3.1 13.9 + - - +
193A PRO 3.8 5.4 - - - +
195A PHE* 1.3 77.3 - - + +
197A ALA* 1.3 64.5 + - - +
199A ARG* 3.3 13.8 + - - +
200A GLU* 3.0 31.6 + - + +
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Residues in contact with ALA 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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165A ALA* 3.7 24.0 - - + +
193A PRO 2.9 17.2 + - - +
194A LEU* 3.7 10.3 - - - +
196A LEU* 1.3 72.9 - - - +
198A ALA* 1.3 56.3 + - - +
201A GLY 2.9 9.7 + - - -
202A SER* 2.7 46.5 + - - +
206A ALA* 3.9 21.3 - - + +
209A LEU* 4.4 1.1 - - + -
238A ILE* 3.5 3.6 - - - +
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Residues in contact with ALA 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 LEU* 2.9 19.0 + - + +
195A PHE 3.5 4.3 - - - +
197A ALA* 1.3 75.2 - - - +
199A ARG* 1.3 63.8 + - - +
200A GLU 3.5 0.2 + - - -
201A GLY 3.6 0.5 + - - -
206A ALA* 5.1 0.6 - - - +
226A PRO* 3.3 36.1 - - + +
229A ILE* 3.9 2.9 - - + -
230A ALA* 3.6 8.9 - - + +
235A HIS* 3.1 21.0 - - - +
238A ILE* 4.0 24.2 - - + -
242A LEU* 4.7 0.4 - - + -
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Residues in contact with ARG 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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189A ARG* 4.1 23.9 - - - +
195A PHE* 2.8 30.6 + - + +
196A LEU* 3.6 18.6 - - - +
198A ALA* 1.3 76.7 - - - +
200A GLU* 1.3 88.3 + - - +
229A ILE* 3.6 21.8 - - + +
233A ARG* 2.8 70.7 + - - +
235A HIS* 2.8 12.6 + - - -
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Residues in contact with GLU 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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166A ALA* 3.4 38.4 - - + +
196A LEU* 3.0 22.7 + - + +
199A ARG* 1.3 113.5 + - + +
201A GLY* 1.3 61.7 + - - +
202A SER* 3.8 5.9 + - - +
233A ARG* 4.4 6.3 + - - +
235A HIS* 3.5 9.0 - - - -
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Residues in contact with GLY 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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168A ASN* 5.3 0.9 + - - -
197A ALA 2.9 5.6 + - - -
199A ARG 3.4 1.0 - - - -
200A GLU* 1.3 79.4 - - - +
202A SER* 1.3 59.9 + - - +
203A TYR* 3.0 11.2 + - - +
235A HIS* 3.4 26.7 + - - -
238A ILE* 3.5 14.1 - - - +
69B ARG* 5.6 0.9 + - - -
75B ARG* 5.9 1.2 + - - -
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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