Contacts of the helix formed by residues 198 - 212 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37J PHE* 4.3 5.2 - - + -
39J THR* 3.6 8.1 - - - +
51J VAL* 4.0 26.7 - - + -
109J ASP* 3.5 7.0 - - - +
193J VAL* 3.8 21.2 - - + +
194J ALA 3.1 12.8 - - - +
195J GLU 3.4 14.1 - - - +
197J THR* 1.3 91.4 - - - +
199J LEU* 1.3 65.7 + - + +
200J THR 3.6 0.4 - - - -
201J ALA* 3.5 5.9 + - - +
202J LEU* 3.2 29.2 + - + +
222J PRO* 4.1 14.6 - - + -
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Residues in contact with LEU 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.8 42.8 - - + -
19J CYS 3.9 10.6 - - - +
20J ASN* 4.7 1.1 - - + -
39J THR* 3.9 11.0 - - + -
48J ILE* 3.8 19.5 - - + -
49J CYS* 3.9 11.9 - - - -
51J VAL* 4.2 14.6 - - + -
105J LEU* 4.1 24.7 - - + +
109J ASP* 3.4 24.9 - - + +
197J THR 3.5 1.8 - - - -
198J PRO* 1.3 77.4 - - + +
200J THR* 1.3 64.3 + - - +
202J LEU* 3.3 8.1 + - + +
203J TYR* 3.1 21.1 + - - +
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Residues in contact with THR 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LEU* 3.9 13.3 - - + +
105J LEU* 3.7 21.5 - - + +
106J GLU* 2.8 53.2 + - + +
109J ASP* 5.1 1.7 + - + +
171J PRO* 3.7 11.4 - - - +
172J LEU* 3.6 22.4 + - + +
197J THR* 4.7 2.3 + - - -
198J PRO 3.6 0.6 + - - -
199J LEU* 1.3 74.9 - - + +
201J ALA* 1.3 57.8 + - - +
203J TYR* 3.2 4.2 + - - +
204J VAL* 3.0 30.8 + - - +
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Residues in contact with ALA 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J ILE* 5.0 2.0 - - + -
171J PRO* 5.2 4.7 - - + +
172J LEU* 4.8 0.2 - - - -
175J GLN* 3.3 41.4 - - + +
193J VAL* 3.5 31.9 - - + -
197J THR 5.2 2.4 + - - +
198J PRO 3.5 5.5 + - - +
199J LEU 3.3 0.6 - - - -
200J THR* 1.3 80.6 + - - +
202J LEU* 1.3 58.3 + - - +
204J VAL 3.3 1.0 + - - -
205J ALA 3.0 22.0 + - - -
220J ILE* 3.5 7.1 - - + +
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Residues in contact with LEU 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J CYS* 3.9 15.9 - - + +
20J ASN* 3.9 22.9 - - - -
21J GLN 3.4 26.9 - - - +
23J PHE* 5.0 0.2 - - + -
28J TRP* 3.0 31.9 - - + -
51J VAL* 4.2 14.6 - - + -
193J VAL* 5.1 0.9 - - + -
198J PRO* 3.2 22.8 + - + +
199J LEU* 3.6 8.7 - - + +
201J ALA* 1.3 73.5 - - - +
203J TYR* 1.3 64.6 + - - +
205J ALA* 3.2 8.8 + - - +
206J ASN 3.4 2.3 + - - -
220J ILE* 3.7 30.5 - - + +
222J PRO* 4.1 10.3 - - + -
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Residues in contact with TYR 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J PHE* 4.6 17.0 - + + -
19J CYS* 4.1 20.1 - - + +
97J ARG* 4.3 3.1 + - - -
98J ASP* 2.7 37.2 + - + -
101J TYR* 3.9 30.1 - + - -
102J LEU* 3.6 24.0 - - + -
105J LEU* 4.6 6.7 - - + -
199J LEU 3.1 12.8 + - - +
200J THR* 3.2 9.2 + - - +
202J LEU* 1.3 76.6 - - - +
204J VAL* 1.3 59.1 + - - +
206J ASN* 3.0 36.6 + - - +
207J LEU* 3.2 29.1 + - + +
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Residues in contact with VAL 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU* 4.5 6.3 - - + -
95J ILE* 4.2 29.2 - - + -
102J LEU* 4.3 13.7 - - + -
172J LEU* 3.4 32.5 - - + -
175J GLN* 3.4 27.1 - - - +
179J LEU* 5.0 2.2 - - + -
200J THR 3.0 8.1 + - - +
201J ALA 3.3 3.1 + - - +
203J TYR* 1.3 72.9 - - - +
205J ALA* 1.3 59.4 + - - +
207J LEU* 3.0 9.3 + - - +
208J ILE* 2.8 39.3 + - + +
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Residues in contact with ALA 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 3.4 43.8 - - + -
28J TRP* 3.9 2.7 - - + -
201J ALA 3.0 12.9 + - - +
202J LEU* 3.2 13.0 - - - +
203J TYR 3.1 0.4 - - - -
204J VAL* 1.3 75.8 - - - +
206J ASN* 1.3 63.0 + - - +
208J ILE* 3.0 25.5 + - + +
209J LYS 3.0 10.4 + - - -
220J ILE* 4.0 12.1 - - + -
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Residues in contact with ASN 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J PHE* 6.3 0.4 - - - +
19J CYS* 4.0 21.6 - - - -
23J PHE* 4.7 0.4 - - - -
28J TRP* 3.1 26.8 + - + -
202J LEU 3.4 2.0 + - - -
203J TYR* 3.0 25.8 + - + +
205J ALA* 1.3 78.7 - - - +
207J LEU* 1.3 58.5 + - + +
209J LYS* 3.2 15.7 + - - +
210J GLU* 2.9 28.4 + - - +
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Residues in contact with LEU 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU* 3.8 12.1 - - + +
94J LEU* 3.2 17.4 - - + +
95J ILE* 3.6 41.5 - - + +
97J ARG* 3.8 14.8 - - - +
98J ASP* 3.6 17.3 - - - +
102J LEU* 4.3 4.9 - - + -
203J TYR* 3.7 36.6 - - + +
204J VAL* 3.0 11.0 + - - +
206J ASN* 1.3 77.4 - - + +
208J ILE* 1.3 56.7 + - - +
210J GLU* 3.8 11.7 - - - +
211J ALA* 2.7 31.7 + - - +
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Residues in contact with ILE 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.9 6.7 - - + -
26J ASN* 4.9 3.6 - - - +
91J LEU* 3.8 23.1 - - + -
175J GLN* 5.3 1.8 - - - +
179J LEU* 3.8 22.4 - - + -
183J LEU* 5.6 0.9 - - + -
204J VAL* 2.8 22.0 + - + +
205J ALA* 3.0 17.0 + - - +
207J LEU* 1.3 76.0 - - - +
209J LYS* 1.3 65.6 + - - +
211J ALA 3.3 7.4 + - - -
212J GLY 3.4 3.1 + - - -
213J PHE* 3.4 42.7 + - + -
218J VAL* 3.7 41.5 - - + +
220J ILE* 5.4 0.7 - - + -
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Residues in contact with LYS 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.2 12.1 - - + -
26J ASN* 2.9 53.4 + - + +
27J GLU* 4.8 5.9 - - - +
28J TRP* 5.5 6.9 - - - +
205J ALA 3.0 11.3 + - - +
206J ASN* 3.3 19.1 - - - +
207J LEU 3.2 0.2 - - - -
208J ILE* 1.3 77.1 - - - +
210J GLU* 1.3 63.4 + - - +
212J GLY* 3.1 15.4 + - - -
213J PHE 4.3 0.9 + - - -
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Residues in contact with GLU 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ARG* 4.6 11.9 + - - +
94J LEU* 3.5 20.6 - - + +
97J ARG* 2.8 45.3 + - - -
206J ASN* 2.9 18.4 + - - +
207J LEU* 3.3 9.0 + - - +
209J LYS* 1.3 77.4 - - - +
211J ALA* 1.3 61.1 + - - +
212J GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J LEU* 3.3 17.0 - - - +
90J ARG* 3.7 26.8 - - + +
91J LEU* 4.0 13.7 - - - +
94J LEU* 3.5 10.7 - - + +
207J LEU 2.7 21.1 + - - +
208J ILE* 3.5 7.2 - - - +
209J LYS 3.2 0.4 - - - -
210J GLU* 1.3 72.9 - - - +
212J GLY* 1.3 58.5 + - - +
213J PHE* 3.7 17.5 - - + -
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Residues in contact with GLY 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J MET* 5.5 0.7 - - - +
87J LEU* 3.8 12.5 - - - +
208J ILE 3.4 0.2 + - - -
209J LYS 3.1 12.3 + - - -
210J GLU 3.2 1.7 - - - -
211J ALA* 1.3 79.4 - - - +
213J PHE* 1.3 67.2 + - - +
214J PRO* 3.3 8.1 - - - +
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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