Contacts of the helix formed by residues 198 - 212 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.3 6.7 - - + -
39A THR* 3.7 7.4 - - - +
51A VAL* 4.1 25.4 - - + -
109A ASP* 3.6 6.5 - - - +
193A VAL* 3.8 19.9 - - + +
194A ALA 3.3 9.4 - - - +
195A GLU 3.3 17.5 - - - +
196A GLN 3.6 1.1 - - - -
197A THR* 1.3 89.4 - - - +
199A LEU* 1.3 65.8 + - + +
200A THR 3.6 0.6 + - - -
201A ALA* 3.6 5.1 + - - +
202A LEU* 3.1 36.3 + - + +
222A PRO* 4.2 9.4 - - + -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.9 24.9 - - + -
19A CYS 4.1 10.5 - - - +
20A ASN* 4.9 0.2 - - + -
39A THR* 4.0 5.6 - - + -
48A ILE* 3.9 28.0 - - + -
49A CYS* 3.7 21.3 - - - -
51A VAL* 4.1 16.6 - - + -
105A LEU* 4.0 24.8 - - + +
109A ASP* 3.1 31.5 + - + +
197A THR 3.6 0.4 - - - -
198A PRO* 1.3 77.0 - - - +
200A THR* 1.3 64.1 + - - +
202A LEU* 3.3 7.5 + - + +
203A TYR* 3.1 20.3 + - - +
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.9 6.4 - - + +
105A LEU* 3.9 19.1 - - + +
106A GLU* 2.8 53.4 + - - +
109A ASP* 4.9 2.4 + - + +
171A PRO* 3.6 12.3 - - - +
172A LEU* 3.5 26.1 - - + +
197A THR* 4.7 3.1 + - - -
199A LEU* 1.3 75.0 - - - +
201A ALA* 1.3 63.5 + - - +
203A TYR* 3.0 5.5 + - - +
204A VAL* 3.0 24.8 + - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 5.2 2.0 - - + -
171A PRO* 5.2 3.8 - - + +
172A LEU* 4.3 0.6 - - - +
175A GLN* 3.2 41.3 - - + +
193A VAL* 3.5 32.8 - - + -
197A THR 5.2 2.4 + - - +
198A PRO 3.6 5.7 + - - +
199A LEU 3.4 0.6 - - - -
200A THR* 1.3 80.3 + - - +
202A LEU* 1.3 56.3 + - - +
204A VAL 3.4 0.7 + - - -
205A ALA 3.1 21.0 + - - -
220A ILE* 3.4 8.7 - - + +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS* 4.0 22.0 - - - +
20A ASN* 4.1 13.2 - - - -
21A GLN 3.4 21.5 - - - +
28A TRP* 3.1 38.5 - - + -
51A VAL* 4.3 9.9 - - + -
193A VAL* 5.0 0.9 - - + -
198A PRO* 3.1 35.3 + - + +
199A LEU* 3.7 6.7 - - + +
200A THR 3.2 0.4 - - - -
201A ALA* 1.3 74.0 - - - +
203A TYR* 1.3 65.7 + - - +
205A ALA* 3.2 9.0 - - - +
206A ASN 3.4 0.2 + - - -
220A ILE* 4.0 27.8 - - + +
222A PRO* 4.2 9.6 - - + -
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.3 12.3 - + + -
19A CYS* 4.2 20.1 - - + +
97A ARG* 4.7 1.6 + - - -
98A ASP* 2.6 33.7 + - + -
101A TYR* 3.8 32.5 - + - -
102A LEU* 3.5 26.5 - - + -
105A LEU* 4.6 6.3 - - + -
199A LEU 3.1 11.7 + - - +
200A THR* 3.0 9.0 + - - +
202A LEU* 1.3 75.6 - - - +
204A VAL* 1.3 58.9 + - - +
206A ASN* 2.9 38.3 + - - +
207A LEU* 3.2 25.4 + - + +
3111A EDO 3.0 25.6 + - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.3 13.2 - - + -
95A ILE* 4.4 20.9 - - + -
102A LEU* 4.4 12.6 - - + -
129A LEU* 6.2 0.2 - - + -
172A LEU* 3.6 21.3 - - + -
175A GLN* 3.4 37.5 - - - +
179A LEU* 5.1 1.3 - - + -
200A THR 3.0 7.5 + - - +
201A ALA 3.6 2.7 - - - +
202A LEU 3.3 0.2 - - - -
203A TYR* 1.3 75.7 - - - +
205A ALA* 1.3 57.3 + - - +
207A LEU* 2.8 10.0 + - - +
208A ILE* 2.8 43.6 + - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.2 47.3 - - + -
28A TRP* 3.8 5.4 - - + -
201A ALA 3.1 12.7 + - - +
202A LEU* 3.2 15.0 - - - +
203A TYR 3.1 0.2 - - - -
204A VAL* 1.3 75.8 - - - +
206A ASN* 1.3 60.0 + - - +
208A ILE* 3.2 12.6 + - - +
209A LYS 3.1 18.0 + - - -
218A VAL* 6.0 0.2 - - + -
220A ILE* 4.0 11.9 - - + -
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 5.5 3.2 - - - +
19A CYS* 3.9 26.9 - - - -
23A PHE* 4.9 0.9 - - - -
28A TRP* 3.4 20.1 + - + -
202A LEU 3.4 1.4 + - - -
203A TYR* 2.9 27.3 + - + +
205A ALA* 1.3 79.6 - - - +
207A LEU* 1.3 57.3 + - + +
209A LYS* 3.2 18.3 + - - +
210A GLU* 3.0 26.0 + - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.8 12.8 - - + -
94A LEU* 3.5 13.1 - - + +
95A ILE* 3.8 40.6 - - + +
97A ARG* 3.5 28.7 - - - +
98A ASP* 3.7 7.0 - - - +
102A LEU* 4.3 5.2 - - + -
203A TYR* 3.9 35.4 - - + +
204A VAL* 2.8 11.0 + - - +
206A ASN* 1.3 75.8 - - + +
208A ILE* 1.3 55.2 + - - +
210A GLU* 3.5 10.3 - - - +
211A ALA* 2.7 35.9 + - - +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.8 7.4 - - + -
26A ASN* 4.9 3.4 - - - +
91A LEU* 3.5 26.9 - - + -
175A GLN* 5.0 1.3 - - - +
179A LEU* 3.6 31.2 - - + -
183A LEU* 5.4 1.1 - - + -
204A VAL* 2.8 22.8 + - + +
205A ALA* 3.4 14.4 - - - +
207A LEU* 1.3 76.1 - - - +
209A LYS* 1.3 63.3 + - - +
211A ALA 3.3 1.2 + - - -
212A GLY 3.3 15.8 + - - -
213A PHE* 3.3 38.3 + - + -
218A VAL* 3.9 30.5 - - + +
220A ILE* 5.7 0.2 - - + -
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Residues in contact with LYS 209 (chain A).
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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23A PHE* 4.1 6.5 - - + -
26A ASN* 3.2 57.3 + - + +
27A GLU* 5.1 3.4 - - - +
28A TRP* 5.6 5.8 - - - +
205A ALA 3.1 12.1 + - - +
206A ASN* 3.4 20.7 + - - +
207A LEU 3.2 0.2 - - - -
208A ILE* 1.3 77.4 - - - +
210A GLU* 1.3 62.6 + - - +
212A GLY* 3.2 13.0 + - - -
213A PHE 4.9 0.4 - - - +
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Residues in contact with GLU 210 (chain A).
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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90A ARG* 4.7 11.0 + - - +
94A LEU* 3.8 13.8 - - + +
97A ARG* 2.8 43.6 + - - -
206A ASN 3.0 13.4 + - - +
207A LEU* 3.2 16.7 + - - +
209A LYS* 1.3 78.6 - - - +
211A ALA* 1.3 62.1 + - - +
212A GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.4 18.1 - - - +
90A ARG* 3.8 26.3 - - + +
91A LEU* 4.0 11.9 - - + +
94A LEU* 3.6 11.2 - - + +
207A LEU 2.7 20.8 + - - +
208A ILE 3.5 7.6 - - - +
209A LYS 3.2 0.2 - - - -
210A GLU* 1.3 73.8 - - - +
212A GLY* 1.3 56.4 + - - +
213A PHE* 3.7 19.7 - - + -
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Residues in contact with GLY 212 (chain A).
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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79A MET* 5.5 0.5 - - - +
87A LEU* 4.0 13.1 - - - +
209A LYS 3.2 10.1 + - - -
210A GLU 3.1 5.3 - - - -
211A ALA* 1.3 79.4 - - - +
213A PHE* 1.3 68.9 + - - +
214A PRO* 3.3 7.3 - - - +
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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