Contacts of the helix formed by residues 204 - 213 (chain C) in PDB entry 4ZZ7
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 204 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 3.1 35.7 + - - -
20C GLN* 4.8 8.9 - - - +
36C LEU* 4.2 6.7 - - + +
37C ALA 5.4 0.4 + - - +
172C LYS* 4.3 0.3 - - - +
175C GLU* 3.6 19.5 - - - +
203C GLY* 1.3 73.8 - - - -
205C LYS* 1.3 69.2 + - - +
206C GLU* 3.1 13.7 + - - +
207C ALA* 3.1 12.5 + - - +
208C VAL* 3.4 12.3 + - - +
501C NAD 4.2 7.6 - - - -
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ASP* 1.3 80.1 + - - +
206C GLU* 1.3 58.7 + - - +
208C VAL* 3.1 1.8 + - - +
209C ASP* 2.8 56.8 + - - +
231C TYR* 3.4 30.2 - - - -
501C NAD 3.3 48.5 + - + +
15E GLU 6.0 1.8 - - - -
16E ASN* 6.2 1.3 - - - -
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Residues in contact with GLU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 2.6 32.7 + - - +
37C ALA 4.6 1.6 - - - +
38C SER* 3.3 21.5 - - - -
39C THR* 3.2 36.6 + - + +
204C ASP* 3.1 12.6 + - - +
205C LYS* 1.3 79.2 - - - +
207C ALA* 1.3 62.4 + - - +
209C ASP* 3.7 6.4 + - + +
210C ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA 4.0 14.2 + - - +
42C VAL* 3.9 21.0 - - + +
172C LYS* 3.8 20.4 - - + -
201C VAL* 4.6 3.4 - - + -
202C ASN 4.8 1.1 - - - +
203C GLY* 4.2 13.9 - - - +
204C ASP* 3.1 9.6 + - - +
206C GLU* 1.3 77.8 - - - +
208C VAL* 1.3 62.8 + - - +
210C ALA* 3.4 4.3 + - - +
211C LEU* 3.3 26.8 + - - +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 3.6 25.1 - - + -
172C LYS* 3.6 25.1 - - + -
204C ASP 3.4 7.4 + - - +
205C LYS 3.1 7.1 + - - +
207C ALA* 1.3 74.9 - - - +
209C ASP* 1.3 67.2 + - - +
211C LEU* 3.1 12.8 + - - +
212C LEU* 3.0 25.7 + - + +
232C ILE* 3.4 31.9 - - + -
501C NAD 3.9 27.6 - - + +
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Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 6.2 0.9 - - + -
205C LYS* 2.8 49.7 + - - +
206C GLU* 3.9 7.4 - - + +
208C VAL* 1.3 73.6 - - - +
210C ALA* 1.3 60.0 + - - +
212C LEU* 3.3 4.8 + - - -
213C HIS* 2.9 38.6 + - + +
231C TYR* 2.6 30.0 + - - -
16E ASN* 4.6 15.2 - - - +
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 3.8 32.0 - - + +
42C VAL* 3.8 17.7 - - + -
43C GLU* 5.6 4.6 - - + +
46C ILE* 4.4 1.6 - - - +
206C GLU 3.2 15.5 + - - +
207C ALA 3.6 5.8 - - - +
208C VAL 3.2 0.8 - - - -
209C ASP* 1.3 78.1 - - - +
211C LEU* 1.3 62.0 + - - +
213C HIS* 3.6 3.1 + - - +
214C ASP* 3.3 25.8 + - - +
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 3.8 14.1 - - + -
46C ILE* 4.1 12.6 - - + -
143C ALA* 4.0 26.2 - - + -
145C ILE* 4.3 17.0 - - + -
170C VAL* 3.7 34.5 - - + +
172C LYS* 3.9 26.9 - - + -
201C VAL* 5.1 1.3 - - + -
207C ALA 3.3 13.9 + - - +
208C VAL* 3.1 9.7 + - - +
210C ALA* 1.3 80.1 - - - +
212C LEU* 1.3 63.9 + - + +
213C HIS 3.3 0.7 + - - -
214C ASP 3.6 4.0 + - - -
217C VAL* 3.6 28.3 - - + +
220C VAL* 5.5 0.2 - - - -
241C LYS* 3.9 0.7 + - - -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 5.0 2.7 - - + -
208C VAL* 3.0 25.1 + - + +
209C ASP 3.3 4.9 + - - +
211C LEU* 1.3 78.9 - - + +
213C HIS* 1.3 64.3 + - - +
214C ASP 3.6 0.4 - - - -
220C VAL* 3.7 37.9 - - + -
231C TYR* 4.1 13.5 - - + +
232C ILE* 3.7 33.4 - - + -
235C THR* 3.9 26.8 - - + +
236C ALA* 4.3 13.7 - - + +
239C ASN* 3.8 12.8 + - - +
241C LYS* 3.4 22.7 + - - +
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Residues in contact with HIS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ASP* 2.9 35.4 + - + +
210C ALA* 3.6 4.0 + - - +
211C LEU 3.2 0.2 - - - -
212C LEU* 1.3 77.6 - - + +
214C ASP* 1.3 61.9 + - - +
215C ASP* 3.8 8.6 + - - +
231C TYR* 4.9 1.8 - - - -
235C THR* 3.8 18.4 - - + +
239C ASN* 3.4 28.0 + - - +
241C LYS* 4.4 0.7 - - - -
16E ASN* 3.1 28.9 + - + -
17E THR 3.4 18.0 + - - -
18E ARG* 5.0 3.6 - - - -
19E SER* 5.9 2.7 - - - -
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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