Contacts of the helix formed by residues 165 - 180 (chain A) in PDB entry 6PAU
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.0 19.1 + - + +
163A LEU 3.8 1.0 - - - +
164A SER* 1.3 76.5 - - - +
166A ALA* 1.3 65.2 + - - +
167A GLU* 2.9 25.9 + - - +
168A VAL* 2.9 32.4 + - + +
169A LEU* 3.0 12.5 + - - +
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Residues in contact with ALA 166 (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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163A LEU 5.0 0.4 - - - -
164A SER 3.4 6.8 + - - +
165A ASP* 1.3 72.2 + - - +
167A GLU* 1.3 58.0 + - - +
169A LEU* 3.4 10.8 + - - +
170A LYS* 2.9 30.7 + - - +
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Residues in contact with GLU 167 (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 ASP* 2.9 16.1 + - - +
166A ALA* 1.3 78.5 - - - +
168A VAL* 1.3 59.7 + - + +
170A LYS* 3.3 7.4 + - - +
171A GLU* 3.0 35.6 + - + +
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Residues in contact with VAL 168 (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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161A LEU* 3.7 46.1 - - + +
162A ASP* 3.7 15.5 - - + +
163A LEU* 4.6 1.3 - - + -
165A ASP* 2.9 28.4 + - + +
167A GLU* 1.3 75.0 - - + +
169A LEU* 1.3 67.4 + - - +
171A GLU* 3.1 16.4 + - + +
172A LEU* 2.9 21.5 + - - +
215A ARG* 4.3 9.2 - - - +
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Residues in contact with LEU 169 (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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163A LEU* 3.6 47.0 - - + +
165A ASP 3.0 10.0 + - - +
166A ALA* 3.8 8.5 - - - +
168A VAL* 1.3 76.2 - - - +
170A LYS* 1.3 57.9 + - - +
172A LEU* 3.3 1.9 + - + +
173A TYR* 2.9 26.7 + - - +
194A PRO* 3.9 37.7 - - + +
197A LEU* 4.3 17.9 - - + -
198A LEU* 3.9 28.7 - - + -
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Residues in contact with LYS 170 (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 2.9 18.5 + - - +
167A GLU* 3.5 6.1 - - - +
169A LEU* 1.3 75.9 - - - +
171A GLU* 1.3 59.7 + - + +
173A TYR* 3.4 16.7 + - + +
174A THR* 2.9 44.3 + - - +
194A PRO* 5.7 4.5 - - + -
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Residues in contact with GLU 171 (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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167A GLU* 3.0 20.8 + - + +
168A VAL* 3.1 21.3 + - + +
170A LYS* 1.3 76.6 - - + +
172A LEU* 1.3 56.5 + - - +
174A THR* 3.3 6.7 + - - -
175A LEU* 2.9 29.3 + - - +
215A ARG* 2.8 43.5 + - - +
220A LYS 4.3 2.4 - - - +
221A LYS* 5.2 0.9 - - - -
222A LEU* 3.8 22.4 + - + +
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Residues in contact with LEU 172 (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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161A LEU* 4.4 6.7 - - + -
163A LEU* 3.8 25.6 - - + -
168A VAL 2.9 12.0 + - - +
169A LEU* 3.7 7.6 - - + +
171A GLU* 1.3 72.9 - - - +
173A TYR* 1.3 68.1 + - - +
175A LEU* 3.2 7.0 + - + +
176A LEU* 3.0 36.5 + - + +
197A LEU* 4.1 15.3 - - + -
201A LEU* 4.0 17.3 - - + -
222A LEU* 3.8 9.1 - - + +
225A PHE* 3.6 54.5 - - + -
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Residues in contact with TYR 173 (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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169A LEU 2.9 17.6 + - - +
170A LYS* 3.6 16.2 - - + +
172A LEU* 1.3 76.7 - - - +
174A THR* 1.3 67.0 + - - +
176A LEU* 3.4 2.3 + - - +
177A ASN* 2.8 50.1 + - + +
191A ASP* 2.9 30.2 + - - -
192A TYR 2.9 30.1 - - - -
193A SER* 4.1 1.6 - - - -
194A PRO* 3.7 35.9 - - + -
197A LEU* 4.0 12.9 - - + +
507A GOL 3.9 7.4 + - - -
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Residues in contact with THR 174 (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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170A LYS* 2.9 31.0 + - - +
171A GLU* 3.6 7.1 - - - -
173A TYR* 1.3 83.2 - - - +
175A LEU* 1.3 69.4 + - - +
177A ASN* 4.4 3.8 - - - -
178A GLU* 3.0 51.5 + - - +
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Residues in contact with LEU 175 (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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171A GLU 2.9 14.2 + - - +
172A LEU* 3.5 12.6 - - + +
174A THR* 1.3 76.0 - - - +
176A LEU* 1.3 59.7 + - + +
179A ASN* 2.9 53.6 + - - +
222A LEU* 3.9 35.7 - - + +
223A VAL* 4.1 15.0 - - - +
224A GLY* 4.1 13.2 - - - +
225A PHE* 3.9 28.7 - - + +
249A CYS* 4.2 15.0 - - + +
251A HIS* 4.3 12.1 - - + +
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Residues in contact with LEU 176 (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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172A LEU* 3.0 32.0 + - + +
173A TYR* 4.0 2.5 - - - +
175A LEU* 1.3 76.9 - - + +
177A ASN* 1.3 61.9 + - - +
180A TYR* 2.9 66.0 + - + +
189A ARG* 4.1 2.4 - - - -
190A PHE 4.2 2.9 - - - +
192A TYR* 4.9 11.9 - - + +
197A LEU* 3.7 41.1 - - + -
225A PHE* 5.3 0.2 - - + -
247A PHE* 3.9 22.9 - - + +
249A CYS* 3.8 17.5 - - + -
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Residues in contact with ASN 177 (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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173A TYR* 2.8 42.1 + - + +
174A THR* 3.9 3.7 - - - +
176A LEU* 1.3 73.1 - - - +
178A GLU* 1.3 69.7 + - - +
189A ARG* 3.0 23.2 + - - +
190A PHE 4.2 8.8 - - - +
191A ASP* 2.8 30.0 + - - +
192A TYR 5.6 1.1 + - - +
406A THR* 3.7 4.5 + - - +
507A GOL 2.5 33.0 + - - -
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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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174A THR* 3.0 38.4 + - + +
177A ASN* 1.3 92.2 - - - +
179A ASN* 1.3 72.8 + - - +
189A ARG* 3.5 25.4 + - - +
251A HIS* 5.2 5.5 + - - -
252A LYS* 3.9 6.8 - - - +
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Residues in contact with ASN 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 LEU* 2.9 32.8 + - - +
178A GLU* 1.3 94.8 + - - +
180A TYR* 1.3 62.5 + - - +
189A ARG* 4.6 0.4 - - - +
249A CYS* 3.5 16.8 - - - -
250A VAL 4.1 3.4 - - - +
251A HIS* 3.6 28.4 + - - -
252A LYS* 3.0 37.8 + - - +
255A ARG* 2.8 33.7 + - - +
502A GOL 3.0 5.6 + - - -
511A 4PS 3.7 1.0 - - - -
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Residues in contact with TYR 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 LEU* 2.9 42.3 + - + +
178A GLU 3.9 0.4 - - - -
179A ASN* 1.3 82.3 - - - +
181A VAL* 1.3 88.3 + - + +
182A GLU* 3.5 4.9 + - - +
189A ARG* 3.8 5.6 - - + +
190A PHE* 4.1 15.7 - + + +
192A TYR* 3.4 41.6 + + - -
246A ASN* 3.3 11.8 + - - -
247A PHE* 3.4 22.3 - + - -
248A LEU 3.6 18.8 - - - -
249A CYS* 3.8 9.2 - - + -
502A GOL 3.2 14.5 - - - -
511A 4PS 3.9 8.1 - - + -
3C LYS* 3.2 29.8 + - - +
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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