Contacts of the helix formed by residues 198 - 212 (chain C) in PDB entry 1ZUM
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 PRO 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 4.3 8.1 - - + -
39C THR* 3.7 5.8 - - - +
51C VAL* 4.0 25.6 - - + -
109C ASP* 3.5 6.5 - - - +
193C VAL* 3.8 20.2 - - + +
194C ALA 3.4 9.6 - - - +
195C GLU 3.4 15.7 - - - +
196C GLN 3.6 1.1 - - - -
197C THR* 1.3 91.4 - - - +
199C LEU* 1.3 67.7 + - + +
200C THR 3.6 0.4 - - - -
201C ALA* 3.5 6.8 + - - +
202C LEU* 3.2 27.1 + - + +
222C PRO* 4.2 14.4 - - + -
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Residues in contact with LEU 199 (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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17C VAL* 3.9 34.8 - - + -
19C CYS 4.0 10.2 - - - +
20C ASN* 4.8 0.2 - - + -
39C THR* 4.0 14.6 - - + -
48C ILE* 4.0 11.0 - - + -
49C CYS* 3.9 10.8 - - - -
51C VAL* 3.8 28.3 - - + -
105C LEU* 4.0 25.9 - - + +
109C ASP* 3.3 27.8 + - + +
198C PRO* 1.3 75.1 - - + +
200C THR* 1.3 66.8 + - - +
202C LEU* 3.1 8.2 + - + +
203C TYR* 3.1 21.3 + - - +
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Residues in contact with THR 200 (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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102C LEU* 4.0 11.5 - - + +
105C LEU* 3.6 22.7 - - + +
106C GLU* 2.8 54.7 + - + +
109C ASP* 4.9 2.6 + - + +
171C PRO* 3.8 11.1 - - - +
172C LEU* 3.4 22.7 - - + +
197C THR* 4.9 2.0 + - - -
198C PRO 3.6 0.6 - - - -
199C LEU* 1.3 73.8 - - + +
201C ALA* 1.3 64.6 + - - +
203C TYR* 3.2 4.3 + - - +
204C VAL* 3.0 25.6 + - - +
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Residues in contact with ALA 201 (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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166C ILE* 5.3 2.0 - - + -
171C PRO* 5.3 4.0 - - + +
172C LEU* 4.8 0.4 - - - -
175C GLN* 3.3 37.5 - - + +
193C VAL* 3.4 33.4 - - + -
197C THR 5.2 2.7 + - - +
198C PRO 3.5 6.8 + - - +
199C LEU 3.3 0.4 - - - -
200C THR* 1.3 82.1 + - - +
202C LEU* 1.3 58.7 + - - +
204C VAL 3.3 0.7 + - - -
205C ALA 3.1 21.0 + - - -
220C ILE* 3.5 7.9 - - + +
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C CYS* 3.8 27.8 - - + +
20C ASN* 3.8 16.6 - - - -
21C GLN 3.5 22.0 - - - +
28C TRP* 3.0 32.5 - - + -
51C VAL* 4.1 15.9 - - + -
193C VAL* 4.9 0.7 - - + -
198C PRO* 3.2 21.1 + - + +
199C LEU* 3.1 8.8 + - + +
201C ALA* 1.3 74.1 - - - +
203C TYR* 1.3 64.5 + - - +
205C ALA* 3.2 9.9 + - - +
220C ILE* 3.7 30.7 - - + +
222C PRO* 4.2 11.2 - - + -
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Residues in contact with TYR 203 (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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18C PHE* 4.2 11.0 - + + -
19C CYS* 4.0 23.3 - - + +
97C ARG* 4.6 1.9 + - - -
98C ASP* 2.7 35.8 + - + -
101C TYR* 3.8 31.9 - + - +
102C LEU* 3.8 22.9 - - + -
105C LEU* 4.5 7.2 - - + -
199C LEU 3.1 12.2 + - - +
200C THR 3.6 7.2 - - - +
202C LEU* 1.3 76.9 - - - +
204C VAL* 1.3 63.4 + - - +
206C ASN* 3.0 31.2 + - + +
207C LEU* 3.2 26.5 + - + +
3115C EDO 3.1 27.1 + - - -
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.5 4.3 - - + -
95C ILE* 4.3 24.9 - - + -
102C LEU* 4.3 17.5 - - + -
129C LEU* 6.3 0.2 - - + -
172C LEU* 3.6 15.5 - - + -
175C GLN* 3.3 35.7 - - - +
179C LEU* 4.9 4.0 - - + -
200C THR 3.0 16.1 + - - +
201C ALA 3.6 2.9 - - - +
203C TYR* 1.3 77.5 - - - +
205C ALA* 1.3 50.7 + - - +
207C LEU* 2.8 10.5 + - - +
208C ILE* 2.8 44.9 + - + +
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Residues in contact with ALA 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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23C PHE* 3.3 46.2 - - + -
28C TRP* 4.0 2.9 - - + -
201C ALA 3.1 6.8 + - - -
202C LEU* 3.3 11.7 - - - +
204C VAL* 1.3 76.4 - - - +
206C ASN* 1.3 62.1 + - - +
208C ILE* 3.1 16.8 + - + +
209C LYS 3.0 18.0 + - - -
220C ILE* 3.8 19.3 - - + -
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Residues in contact with ASN 206 (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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18C PHE* 6.0 1.4 - - - +
19C CYS* 3.9 23.6 - - - -
23C PHE* 4.8 0.9 - - - -
28C TRP* 3.0 27.7 + - + -
202C LEU 3.4 1.6 + - - -
203C TYR* 3.0 24.8 + - + +
205C ALA* 1.3 80.8 - - - +
207C LEU* 1.3 56.8 + - + +
209C LYS* 3.3 15.0 + - - +
210C GLU* 3.0 26.9 + - - +
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Residues in contact with LEU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.8 11.4 - - + +
94C LEU* 3.7 13.4 - - + +
95C ILE* 3.7 41.3 - - + +
97C ARG* 3.6 15.7 - - - +
98C ASP* 3.4 19.7 - - - +
102C LEU* 4.3 4.9 - - + -
203C TYR* 3.2 36.2 + - + +
204C VAL* 2.8 10.7 + - - +
206C ASN* 1.3 79.1 - - + +
208C ILE* 1.3 59.4 + - - +
210C GLU* 3.3 12.2 + - - +
211C ALA* 2.8 31.2 + - - +
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Residues in contact with ILE 208 (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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23C PHE* 4.9 1.6 - - + -
26C ASN* 4.9 8.1 - - - +
91C LEU* 3.8 25.1 - - + -
175C GLN* 5.1 2.0 - - - +
179C LEU* 3.9 22.0 - - + -
183C LEU* 5.7 0.7 - - + -
204C VAL* 2.8 21.7 + - + +
205C ALA* 3.1 17.7 + - - +
207C LEU* 1.3 76.5 - - - +
209C LYS* 1.3 65.3 + - - +
211C ALA 3.3 6.8 + - - -
212C GLY 3.4 7.4 + - - -
213C PHE* 3.4 38.3 + - + +
218C VAL* 3.6 42.2 - - + +
220C ILE* 5.2 0.2 - - + -
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Residues in contact with LYS 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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23C PHE* 4.3 6.5 - - + -
26C ASN* 3.4 55.2 + - + +
27C GLU* 5.5 2.4 - - - +
28C TRP* 5.8 6.3 - - - +
205C ALA 3.0 11.7 + - - +
206C ASN* 3.4 17.0 - - - +
207C LEU 3.2 0.2 - - - -
208C ILE* 1.3 77.5 - - - +
210C GLU* 1.3 64.0 + - - +
212C GLY* 3.0 15.9 + - - -
213C PHE 4.9 0.6 - - - +
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Residues in contact with GLU 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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90C ARG* 4.6 11.9 + - - +
94C LEU* 3.8 15.1 - - + +
97C ARG* 2.8 43.4 + - - -
206C ASN* 3.0 16.0 + - - +
207C LEU* 3.3 15.1 + - - +
209C LYS* 1.3 78.5 - - - +
211C ALA* 1.3 60.2 + - - +
212C GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 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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87C LEU* 3.5 16.0 - - - +
90C ARG* 3.8 33.5 - - + +
91C LEU* 4.0 18.4 - - + +
94C LEU* 3.7 4.2 - - + +
207C LEU 2.8 17.2 + - - +
208C ILE 3.6 7.4 - - - +
209C LYS 3.2 0.4 - - - -
210C GLU* 1.3 76.2 - - - +
212C GLY* 1.3 59.0 + - - +
213C PHE* 4.1 14.6 - - + -
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Residues in contact with GLY 212 (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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87C LEU* 4.2 11.4 - - - +
209C LYS 3.0 13.7 + - - -
210C GLU 3.2 1.5 - - - -
211C ALA* 1.3 80.9 - - - +
213C PHE* 1.3 67.9 + - - +
214C PRO* 3.4 5.9 - - - +
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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
------------------------------------------------------------
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