Contacts of the helix formed by residues 174 - 184 (chain D) in PDB entry 2ZSU
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 SER 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D VAL* 5.8 0.7 - - - +
171D MET* 2.9 49.1 + - - -
172D LEU 3.5 0.6 - - - -
173D PHE* 1.3 80.3 - - - +
175D GLU* 1.3 65.1 + - - +
176D GLU* 3.9 7.8 + - - +
177D PHE* 3.1 14.7 + - - +
178D TYR* 3.0 26.2 + - - -
211D LYS* 4.4 7.0 - - - +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 1.3 74.9 - - - +
176D GLU* 1.3 63.6 + - - +
178D TYR* 3.2 10.6 + - - +
179D LYS* 3.0 59.4 + - + +
211D LYS* 4.0 22.2 - - + +
214D LYS* 4.4 22.9 + - - +
215D VAL* 5.0 7.9 - - + -
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLU* 3.3 22.3 - - - +
174D SER* 3.3 6.3 + - - +
175D GLU* 1.3 80.0 - - - +
177D PHE* 1.3 62.2 + - - +
179D LYS* 3.6 11.5 + - + +
180D ASN* 3.0 38.9 + - - +
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ILE* 3.7 30.5 - - + -
146D VAL* 4.1 20.9 - - + -
149D ILE* 3.6 31.6 - - + -
158D ILE* 5.7 0.4 - - + -
160D VAL* 4.2 6.5 - - + -
171D MET 3.4 20.6 - - - +
172D LEU* 2.9 44.2 - - + -
174D SER* 3.1 9.6 + - - +
176D GLU* 1.3 77.8 - - - +
178D TYR* 1.3 64.4 + + - +
180D ASN* 3.2 5.9 + - - +
181D ALA* 2.8 30.2 + - + +
191D TYR* 3.3 26.9 - + - -
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Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LEU 3.9 3.5 + - - -
173D PHE* 3.3 55.7 - - - -
174D SER 3.0 21.5 + - - -
175D GLU* 3.2 5.4 + - - +
177D PHE* 1.3 76.4 - + - +
179D LYS* 1.3 64.2 + - - +
181D ALA* 3.7 2.5 - - - +
182D TYR* 2.9 27.4 + - - +
191D TYR* 3.6 27.1 + + - -
193D THR* 4.6 2.6 - - - +
208D ALA* 3.6 16.8 - - + +
211D LYS* 4.0 15.3 - - + -
212D MET* 3.5 40.8 - - + -
215D VAL* 3.6 15.1 - - + +
216D PHE* 3.9 19.3 - + + -
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D GLU* 3.0 47.4 + - + +
176D GLU* 3.7 12.1 - - + +
178D TYR* 1.3 77.7 - - - +
180D ASN* 1.3 65.3 + - - +
182D TYR* 3.6 4.0 + - - +
183D ARG* 3.3 22.4 + - - +
215D VAL* 3.8 24.4 - - + +
187E ASP* 5.4 5.1 + - - -
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Residues in contact with ASN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D VAL* 6.1 1.2 - - - +
149D ILE* 3.7 23.4 - - + +
150D GLU* 3.7 26.4 + - - +
176D GLU* 3.0 33.3 + - - +
177D PHE* 3.7 5.9 - - - +
178D TYR 3.2 0.2 - - - -
179D LYS* 1.3 79.3 - - - +
181D ALA* 1.3 59.4 + - - +
183D ARG* 2.9 41.8 + - - +
184D ALA* 3.0 12.8 + - - +
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Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ILE* 4.0 15.7 - - + +
158D ILE* 3.6 6.0 - - + +
177D PHE* 2.8 25.3 + - + +
178D TYR* 3.7 7.9 - - - +
180D ASN* 1.3 72.4 - - - +
182D TYR* 1.3 64.9 + - - +
184D ALA* 3.1 12.7 + - - +
185D LEU* 3.2 17.2 + - - +
191D TYR* 3.9 33.2 - - + -
216D PHE* 4.3 3.4 - - + -
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Residues in contact with TYR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D TYR 2.9 16.6 + - - +
179D LYS 3.8 3.6 - - - +
181D ALA* 1.3 76.9 - - - +
183D ARG* 1.3 67.5 + - + +
185D LEU* 3.0 14.3 + - - +
215D VAL* 3.5 26.7 - - + -
216D PHE* 3.7 33.1 - + + -
217D ASP* 2.8 37.8 + - - -
239D VAL 4.0 1.8 - - - -
240D LYS* 3.1 58.1 - - + +
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Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ILE 2.9 19.4 + - - -
150D GLU* 2.8 32.7 + - - +
152D ASN 3.5 5.5 + - - -
153D SER* 4.1 3.7 - - - -
179D LYS 3.3 11.5 + - - +
180D ASN* 2.9 38.9 + - - +
182D TYR* 1.3 85.3 - - + +
184D ALA* 1.3 66.8 + - - +
185D LEU 3.1 0.4 + - - -
240D LYS* 3.6 9.0 + - - +
153E SER* 2.8 20.2 + - - -
154E GLY* 4.6 1.0 - - - +
183E ARG* 2.7 76.0 + - + +
240E LYS* 5.9 2.5 - - - +
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ILE* 3.6 24.9 - - + -
152D ASN 3.7 6.1 - - - +
153D SER* 3.5 12.6 - - - -
154D GLY 2.6 27.0 + - - -
155D PHE* 3.1 9.4 + - + -
158D ILE* 4.0 6.7 - - + -
180D ASN 3.0 18.5 + - - +
181D ALA 3.1 8.5 + - - +
183D ARG* 1.3 86.5 - - - +
185D LEU* 1.3 57.1 + - - +
183E ARG* 4.1 0.2 - - - -
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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