Contacts of the helix formed by residues 230 - 235 (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 LYS 230 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Z CYS* 4.3 7.4 - - + -
129Z ALA 6.1 0.4 - - - +
165Z ASP* 5.6 3.4 + - - -
178Z SER* 2.8 28.6 + - - +
179Z ASN 2.8 18.8 + - - +
180Z MET 3.9 16.3 + - - -
181Z PHE* 3.9 24.0 - - + -
210Z GLN* 4.9 1.3 - - - +
228Z TYR 3.5 2.4 + - - -
229Z THR* 1.3 66.4 - - - +
231Z VAL* 1.3 64.5 + - - +
232Z CYS* 3.5 26.9 - - - -
233Z ASN* 3.3 29.4 + - - +
234Z TYR* 3.3 9.1 - - - -
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Residues in contact with VAL 231 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Z VAL* 5.7 0.9 - - + -
103Z ILE* 5.0 2.9 - - + -
123Z LEU* 4.6 2.9 - - + -
124Z PRO* 3.9 11.0 - - + -
209Z LEU* 3.2 35.7 - - + +
210Z GLN 2.8 24.4 + - - +
211Z GLY* 3.7 6.5 - - - -
212Z ILE* 3.5 35.4 - - + -
229Z THR* 3.7 7.2 - - + +
230Z LYS* 1.3 66.7 - - - +
232Z CYS* 1.3 51.5 + - - +
233Z ASN 3.0 4.3 - - - -
234Z TYR* 2.8 36.2 + - - +
235Z VAL* 3.7 4.6 + - + +
238Z ILE* 4.6 17.7 - - + -
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Residues in contact with CYS 232 (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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124Z PRO* 3.7 23.9 - - + +
127Z SER* 4.2 2.2 - - - -
128Z CYS* 2.0 63.0 - - - +
210Z GLN* 3.9 5.7 + - - +
230Z LYS* 3.5 23.1 - - - -
231Z VAL* 1.3 74.0 - - - +
233Z ASN* 1.3 62.8 + - - +
234Z TYR 3.3 1.0 + - - -
235Z VAL* 3.9 13.7 + - - +
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Residues in contact with ASN 233 (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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128Z CYS* 4.5 3.1 - - - -
178Z SER* 2.9 25.5 + - - -
179Z ASN* 2.7 33.4 + - - +
230Z LYS* 3.3 29.5 + - - +
231Z VAL 2.9 0.2 + - - -
232Z CYS* 1.3 83.3 - - - +
234Z TYR* 1.3 65.1 + - + +
235Z VAL 3.5 0.7 - - - -
236Z SER* 5.9 1.7 - - - -
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Residues in contact with TYR 234 (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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91Z HIS* 3.6 37.0 - + - -
101Z ASN* 2.5 33.7 + - - -
103Z ILE* 3.7 36.3 - - + -
179Z ASN* 3.2 25.3 - - + +
229Z THR* 3.8 15.0 - - + -
230Z LYS 3.3 27.4 - - - -
231Z VAL* 2.8 16.8 + - - +
233Z ASN* 1.3 83.4 - - + +
235Z VAL* 1.3 61.5 - - - +
236Z SER* 3.0 4.0 - - - -
237Z TRP* 3.0 13.7 + + + +
238Z ILE* 2.8 34.1 + - + +
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Residues in contact with VAL 235 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123Z LEU* 4.3 17.0 - - + +
124Z PRO* 3.3 44.9 - - + +
231Z VAL* 3.8 12.3 - - + +
232Z CYS* 3.9 14.3 + - - +
233Z ASN 3.5 1.0 - - - -
234Z TYR* 1.3 79.1 - - - +
236Z SER* 1.3 58.8 + - - +
238Z ILE* 3.7 2.6 - - - +
239Z LYS* 3.0 54.3 + - + +
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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