Contacts of the helix formed by residues 175 - 185 (chain D) in PDB entry 1ZSV
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 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D VAL* 3.1 21.8 - - - +
174D GLY* 1.3 78.4 - - - +
176D ASP* 1.3 58.4 + - - +
177D GLU* 3.4 12.2 - - - +
178D LYS* 3.1 36.9 + - - +
179D VAL* 3.2 11.6 + - - +
192D ASN* 3.5 10.5 - - - +
319D GLY 5.7 2.9 - - - -
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Residues in contact with ASP 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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175D SER* 1.3 70.8 - - - +
177D GLU* 1.3 63.8 + - - +
178D LYS 3.3 0.4 - - - -
179D VAL* 3.7 14.8 - - - +
180D ALA* 3.1 21.1 + - - +
192D ASN* 3.3 29.2 + - - +
195D THR* 3.8 14.1 + - - +
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Residues in contact with GLU 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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175D SER* 3.4 10.9 + - - +
176D ASP* 1.3 77.6 - - - +
178D LYS* 1.3 57.6 + - + +
180D ALA* 3.2 8.7 + - - +
181D TYR* 3.0 27.5 + - - +
322D LEU* 3.6 30.6 - - + +
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Residues in contact with LYS 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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151D ALA* 3.8 20.1 + - + -
173D VAL* 3.1 20.4 - - + -
174D GLY* 4.2 4.8 - - - +
175D SER* 3.1 26.3 + - - +
177D GLU* 1.3 77.3 - - - +
179D VAL* 1.3 64.4 + - - +
181D TYR* 3.8 6.4 - - - +
182D LEU* 3.2 30.8 + - - +
319D GLY* 3.6 27.4 + - - -
320D ASP 5.3 0.9 - - - -
321D ASN 3.6 26.1 + - - -
322D LEU* 4.0 16.8 - - + +
421D CL 3.7 28.5 - - + +
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Residues in contact with VAL 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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173D VAL* 3.9 4.3 - - + -
175D SER 3.2 16.3 + - - +
176D ASP* 3.7 18.6 - - - +
177D GLU 3.3 0.2 - - - -
178D LYS* 1.3 76.8 - - - +
180D ALA* 1.3 62.7 + - - +
183D GLN* 3.1 51.1 + - - +
190D VAL* 3.9 22.5 - - + +
191D PHE* 3.8 29.4 - - - +
192D ASN* 3.8 9.4 - - + +
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Residues in contact with ALA 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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176D ASP 3.1 12.7 + - - +
177D GLU* 3.2 11.6 + - - +
179D VAL* 1.3 78.9 - - - +
181D TYR* 1.3 61.7 + - - +
183D GLN* 3.4 14.8 + - - +
184D LYS* 3.2 19.8 + - - +
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Residues in contact with TYR 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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151D ALA* 5.2 2.9 - - + -
156D SER* 5.5 5.2 - - - -
177D GLU 3.0 15.6 + - - +
178D LYS* 3.8 4.5 - - - +
179D VAL 3.3 0.6 - - - -
180D ALA* 1.3 76.9 - - - +
182D LEU* 1.3 72.2 + - + +
184D LYS* 3.1 26.6 + - + +
185D LEU* 3.1 61.1 + - + +
297D GLN* 4.1 6.9 + - - +
298D TYR* 3.8 13.9 + - - -
299D LYS* 3.6 41.1 + - + +
322D LEU* 3.8 31.2 - - + -
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Residues in contact with LEU 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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150D ALA* 3.5 27.1 - - + +
151D ALA* 4.1 9.9 - - + -
156D SER* 4.6 2.9 - - - -
173D VAL* 3.4 31.0 - - + -
178D LYS 3.2 13.5 + - - +
181D TYR* 1.3 91.9 - - + +
183D GLN* 1.3 60.4 + - - +
184D LYS 3.2 0.2 - - - -
185D LEU* 3.3 12.1 + - + +
186D GLY 3.1 8.3 + - - -
187D PHE* 3.0 51.8 + - + +
190D VAL* 3.7 23.3 - - + -
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Residues in contact with GLN 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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179D VAL* 3.1 32.0 - - - +
180D ALA* 3.5 15.0 - - - +
182D LEU* 1.3 78.0 - - - +
184D LYS* 1.3 61.4 + - - +
186D GLY* 3.2 12.0 + - - -
187D PHE 4.7 9.4 - - - +
190D VAL* 4.3 20.7 + - + +
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Residues in contact with LYS 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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180D ALA 3.2 9.5 + - - +
181D TYR* 3.1 36.9 + - + +
183D GLN* 1.3 78.3 - - - +
185D LEU* 1.3 61.5 + - + +
186D GLY* 3.1 5.9 + - - -
297D GLN* 4.6 13.4 + - - +
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Residues in contact with LEU 185 (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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156D SER* 5.0 3.4 - - - -
160D GLN* 3.4 43.2 - - + +
163D LYS* 5.1 4.9 - - - +
181D TYR* 3.1 57.0 + - + +
182D LEU* 3.3 18.8 + - + +
184D LYS* 1.3 79.3 - - + +
186D GLY* 1.3 60.1 + - - +
187D PHE* 3.6 10.0 + - + -
297D GLN* 3.4 35.4 - - + +
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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