Contacts of the helix formed by residues 164 - 176 (chain Z) in PDB entry 4TPI
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 164 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132Z ALA* 3.7 22.3 - - - +
163Z LEU* 1.3 79.1 - - - +
165Z ASP* 1.3 66.0 + - - +
166Z SER* 3.7 6.4 + - - -
167Z SER* 2.8 29.4 + - - -
168Z CYS* 2.9 21.7 + - - +
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Residues in contact with ASP 165 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Z LEU 3.7 1.8 + - - -
164Z SER* 1.3 75.6 - - - +
166Z SER* 1.3 64.8 + - - +
168Z CYS* 3.4 6.6 + - - +
169Z LYS* 2.8 69.0 + - - +
176Z ILE* 5.3 4.4 - - - +
177Z THR 5.3 1.7 - - - +
178Z SER* 5.9 2.4 - - - -
180Z MET 5.5 2.8 - - - +
230Z LYS* 5.6 3.3 + - - -
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Residues in contact with SER 166 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164Z SER* 3.0 7.2 + - - -
165Z ASP* 1.3 85.5 + - - +
167Z SER* 1.3 57.5 + - - +
169Z LYS* 3.2 8.0 + - - +
170Z SER* 3.1 31.0 + - - -
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Residues in contact with SER 167 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Z LEU* 3.7 12.5 - - - +
164Z SER* 2.8 34.1 + - - -
166Z SER* 1.3 76.1 - - - +
168Z CYS* 1.3 74.0 + - - +
170Z SER* 3.0 10.1 + - - -
171Z ALA* 2.8 23.9 + - - +
185Z LEU* 5.3 14.7 - - - +
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Residues in contact with CYS 168 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Z LEU* 5.3 0.7 - - - +
164Z SER 2.9 14.8 + - - +
165Z ASP* 3.5 8.7 - - - +
167Z SER* 1.3 81.2 + - - +
169Z LYS* 1.3 57.9 + - - +
171Z ALA* 3.1 6.5 + - - +
172Z TYR* 2.9 24.6 + - - -
176Z ILE* 3.8 33.5 - - + +
181Z PHE* 4.1 3.4 - - - -
182Z CYS* 2.0 63.0 - - + +
225Z PRO* 5.4 1.1 - - - -
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Residues in contact with LYS 169 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Z ASP* 2.8 50.3 + - - +
166Z SER* 3.7 6.3 - - - +
167Z SER 3.1 0.4 - - - -
168Z CYS* 1.3 76.9 - - - +
170Z SER* 1.3 57.2 + - - +
172Z TYR 3.9 6.3 - - - +
173Z PRO* 3.2 29.6 - - - +
174Z GLY 4.6 1.1 + - - +
176Z ILE* 3.9 37.5 - - + +
177Z THR 5.1 4.3 - - - -
178Z SER* 6.3 1.0 - - - +
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Residues in contact with SER 170 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166Z SER 3.1 13.3 + - - -
167Z SER* 3.0 11.7 + - - -
169Z LYS* 1.3 76.4 - - - +
171Z ALA* 1.3 67.8 + - - +
172Z TYR 3.4 0.7 + - - -
173Z PRO* 3.4 13.8 - - - +
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Residues in contact with ALA 171 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Z SER 2.8 12.5 + - - +
168Z CYS 3.7 7.0 - - - +
170Z SER* 1.3 77.7 - - - +
172Z TYR* 1.3 70.0 + - + +
173Z PRO* 3.2 7.6 - - - +
185Z LEU* 5.0 5.2 - - + -
223Z ASN* 3.3 28.0 - - - +
224Z LYS* 5.2 3.1 - - - +
225Z PRO* 3.5 26.0 - - + -
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Residues in contact with TYR 172 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168Z CYS 2.9 15.6 + - - -
169Z LYS* 3.4 7.0 - - - +
171Z ALA* 1.3 81.9 - - + +
173Z PRO* 1.3 69.3 - - - +
174Z GLY 3.3 2.4 + - - -
175Z GLN* 3.4 36.5 + - - +
176Z ILE* 3.6 24.5 + - + +
182Z CYS* 4.4 3.6 - - - -
215Z TRP* 3.8 13.5 - + - -
216Z GLY* 3.5 1.3 - - - -
217Z SER* 3.0 38.3 + - - -
224Z LYS* 3.4 19.8 - - + +
225Z PRO* 2.8 35.1 + - + -
227Z VAL* 3.5 29.8 - - + -
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Residues in contact with PRO 173 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169Z LYS 3.2 13.0 - - - +
170Z SER* 3.4 11.7 - - - +
171Z ALA 3.2 11.0 - - - +
172Z TYR* 1.3 86.9 - - - +
174Z GLY* 1.3 62.5 + - - +
175Z GLN* 3.4 16.8 + - - +
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Residues in contact with GLY 174 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169Z LYS* 4.6 2.0 + - - +
172Z TYR 3.3 1.2 + - - -
173Z PRO* 1.3 72.0 - - - +
175Z GLN* 1.3 63.0 + - - +
176Z ILE 3.9 1.8 - - - -
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Residues in contact with GLN 175 (chain Z).
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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39I ARG* 5.4 14.2 - - - +
98Z THR 4.5 4.7 - - - +
172Z TYR* 3.4 29.6 + - + +
173Z PRO* 3.3 15.6 - - - +
174Z GLY* 1.3 84.0 - - - +
176Z ILE* 1.3 64.0 + - - +
177Z THR* 3.9 4.8 + - - +
180Z MET* 3.8 16.8 - - - +
215Z TRP* 3.5 31.9 - - + -
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Residues in contact with ILE 176 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Z ASP* 5.3 3.4 - - - +
168Z CYS* 3.8 34.3 - - + +
169Z LYS* 3.9 34.3 - - + +
172Z TYR* 3.6 27.1 + - + +
174Z GLY 4.9 0.5 - - - +
175Z GLN* 1.3 80.2 + - - +
177Z THR* 1.3 72.6 + - - +
180Z MET* 4.0 15.3 - - + +
215Z TRP* 3.9 14.8 - - + -
227Z VAL* 3.8 28.0 - - + -
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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