Contacts of the helix formed by residues 176 - 190 (chain A) in PDB entry 4UY3
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 LYS 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A THR* 3.1 22.7 + - - +
173A GLU* 3.2 37.1 + - - +
174A ILE 3.1 0.6 - - - -
175A GLU* 1.3 74.3 - - + +
177A PHE* 1.3 63.0 + - + +
178A GLU 3.4 0.4 - - - -
179A PRO* 3.6 14.0 - - + +
180A ARG* 3.4 23.9 - - - +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A TYR* 4.1 9.6 - + + -
152A MET* 3.6 27.1 - - + -
173A GLU* 4.0 12.6 - - + -
174A ILE* 3.0 22.5 + - + +
176A LYS* 1.3 82.9 - - + +
178A GLU* 1.3 64.7 + - - +
179A PRO 3.5 0.2 - - - -
180A ARG* 3.2 23.8 + - - +
181A LEU* 3.0 26.6 + - + +
203A LEU* 3.7 20.4 - - + +
206A GLN* 4.4 10.3 - - + -
207A MET* 3.8 44.0 - - + -
210A LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 178 (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 TYR* 3.5 35.3 + - + +
174A ILE 4.0 1.4 + - - -
175A GLU 3.0 10.5 + - - +
177A PHE* 1.3 73.8 - - - +
179A PRO* 1.3 74.1 - - + +
181A LEU* 3.0 23.4 + - + +
182A GLU* 3.3 26.0 + - + +
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Residues in contact with PRO 179 (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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175A GLU 3.2 13.0 - - - +
176A LYS* 3.6 15.7 - - + +
178A GLU* 1.3 92.7 - - + +
180A ARG* 1.3 57.1 + - + +
182A GLU* 3.2 18.2 + - + +
183A GLN* 2.9 45.6 + - - +
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Residues in contact with ARG 180 (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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176A LYS* 3.4 20.6 - - - +
177A PHE* 3.2 22.5 + - - +
178A GLU 3.1 0.8 - - - -
179A PRO* 1.3 74.4 - - + +
181A LEU* 1.3 65.2 + - - +
183A GLN* 3.8 21.3 - - - +
184A TYR* 3.4 6.4 + - - +
199A HIS* 2.9 37.5 + - + +
202A ALA* 4.2 8.7 - - - +
203A LEU* 3.7 51.1 - - + +
206A GLN* 2.7 32.3 + - - -
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Residues in contact with LEU 181 (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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142A TYR* 3.8 29.8 - - + +
145A CYS* 3.9 18.6 - - + -
146A LYS* 4.1 17.3 - - + +
149A TYR* 4.2 34.8 - - + -
177A PHE* 3.0 20.4 + - + +
178A GLU* 3.0 11.6 + - + +
180A ARG* 1.3 74.7 - - - +
182A GLU* 1.3 68.2 + - + +
184A TYR* 2.9 21.0 + - - +
185A GLU* 3.3 8.7 + - - +
200A ILE* 4.8 0.7 - - + -
203A LEU* 3.8 20.4 - - + -
207A MET* 5.7 0.7 - - + -
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Residues in contact with GLU 182 (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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178A GLU* 3.3 23.6 + - + +
179A PRO* 3.2 21.2 + - + +
181A LEU* 1.3 75.3 - - + +
183A GLN* 1.3 63.4 + - - +
185A GLU* 2.9 25.8 + - - +
186A VAL* 3.2 16.2 + - + +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PRO* 2.9 41.2 + - - +
180A ARG* 3.6 19.3 - - - +
182A GLU* 1.3 75.7 - - - +
184A TYR* 1.3 62.7 + - - +
186A VAL* 3.2 9.8 + - - +
187A LEU* 3.1 28.9 + - + +
199A HIS* 3.4 25.1 - - + +
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Residues in contact with TYR 184 (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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138A ASN* 3.3 35.8 - - + +
139A ASP* 2.5 27.5 + - - -
142A TYR* 3.4 37.0 - + + -
180A ARG 3.4 4.0 + - - +
181A LEU 2.9 10.5 + - - +
183A GLN* 1.3 77.9 - - - +
185A GLU* 1.3 69.9 + - + +
186A VAL 3.1 0.3 + - - -
187A LEU* 3.2 4.6 + - - +
188A LYS* 2.9 43.2 + - + +
196A ALA* 3.8 40.6 - - + -
199A HIS* 4.0 16.7 + + + -
200A ILE* 4.0 19.7 - - + -
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Residues in contact with GLU 185 (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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142A TYR* 3.3 33.7 + - + +
181A LEU 3.8 11.9 - - - +
182A GLU* 2.9 14.3 + - - +
184A TYR* 1.3 81.3 - - + +
186A VAL* 1.3 58.3 + - + +
188A LYS* 3.8 6.6 - - - +
189A ALA* 3.0 31.8 + - - +
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Residues in contact with VAL 186 (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 GLU* 3.2 12.9 + - + +
183A GLN* 3.5 11.0 - - - +
184A TYR 3.1 0.4 - - - -
185A GLU* 1.3 74.9 - - + +
187A LEU* 1.3 65.4 + - + +
189A ALA* 3.4 5.6 + - - +
190A ASP* 2.9 50.0 + - - +
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Residues in contact with LEU 187 (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 GLN* 3.1 20.6 + - + +
184A TYR* 3.7 5.8 - - - +
186A VAL* 1.3 77.8 - - + +
188A LYS* 1.3 63.9 + - - +
190A ASP* 3.4 10.2 + - - +
192A ASN* 2.9 39.7 + - + +
195A GLN* 3.8 32.8 - - + +
196A ALA* 4.0 18.2 - - + +
199A HIS* 3.8 39.3 - - + +
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Residues in contact with LYS 188 (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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57A ASN* 2.9 24.9 + - - +
135A TYR* 4.5 22.5 + - + -
139A ASP* 3.1 39.0 + - - +
184A TYR* 2.9 38.7 + - + +
185A GLU* 3.8 6.1 - - - +
187A LEU* 1.3 77.1 - - - +
189A ALA* 1.3 54.2 + - - +
191A GLY* 2.7 25.6 + - - -
192A ASN 4.8 2.2 - - - +
193A TYR* 5.7 1.1 - - - +
196A ALA* 4.4 7.7 - - + +
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Residues in contact with ALA 189 (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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57A ASN* 3.7 17.2 - - - +
59A LYS* 3.5 17.5 + - - -
185A GLU 3.0 20.0 + - - +
186A VAL* 3.6 7.9 - - - +
188A LYS* 1.3 77.7 - - - +
190A ASP* 1.3 62.0 + - - +
191A GLY 3.2 1.3 + - - -
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Residues in contact with ASP 190 (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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59A LYS* 3.2 36.0 - - - +
60A GLY* 3.3 8.1 + - - -
186A VAL* 2.9 36.8 + - - +
187A LEU* 3.8 4.0 + - - +
188A LYS 3.1 0.6 - - - -
189A ALA* 1.3 80.4 - - - +
191A GLY* 1.3 61.0 + - - +
192A ASN* 3.4 20.3 + - - +
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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