Contacts of the helix formed by residues 198 - 212 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H PHE* 4.4 4.7 - - + -
39H THR* 3.6 8.5 - - - +
51H VAL* 3.9 27.4 - - + -
109H ASP* 3.4 9.6 - - - +
193H VAL* 3.9 20.0 - - + +
194H ALA 3.1 12.1 - - - +
195H GLU 3.4 14.1 - - - +
196H GLN 3.5 1.1 - - - -
197H THR* 1.3 90.1 - - - +
199H LEU* 1.3 64.4 + - + +
200H THR 3.7 0.4 - - - -
201H ALA* 3.6 6.3 + - - +
202H LEU* 3.1 34.1 + - + +
222H PRO* 4.4 9.4 - - + -
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Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H VAL* 3.8 24.0 - - + -
19H CYS 3.7 21.6 - - - +
20H ASN* 4.6 1.3 - - + -
39H THR* 3.7 23.3 - - + -
48H ILE* 3.8 22.7 - - + -
49H CYS* 3.8 11.7 - - - -
51H VAL* 4.1 15.0 - - + -
105H LEU* 4.1 22.9 - - + +
109H ASP* 3.5 21.3 + - - +
198H PRO* 1.3 75.4 - - + +
200H THR* 1.3 66.7 + - - +
202H LEU* 3.2 6.1 + - + +
203H TYR* 3.1 21.7 + - - +
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Residues in contact with THR 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LEU* 3.8 13.5 - - + +
105H LEU* 3.8 20.0 - - + +
106H GLU* 2.8 53.9 + - - +
109H ASP* 5.0 2.3 + - + +
171H PRO* 3.7 11.8 - - - +
172H LEU* 3.5 22.6 + - + +
197H THR* 4.6 2.6 + - - -
199H LEU* 1.3 75.3 - - + +
201H ALA* 1.3 63.1 + - - +
203H TYR* 3.2 4.7 + - - +
204H VAL* 3.0 25.6 + - - +
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Residues in contact with ALA 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ILE* 5.3 1.6 - - + -
171H PRO* 5.3 4.0 + - + +
172H LEU* 4.5 0.4 - - - +
175H GLN* 3.3 39.3 - - + +
193H VAL* 3.4 33.9 - - + -
197H THR 5.1 2.9 + - - +
198H PRO 3.6 5.7 + - - +
199H LEU 3.3 0.6 - - - -
200H THR* 1.3 80.4 + - - +
202H LEU* 1.3 58.1 + - - +
204H VAL 3.3 0.7 + - - -
205H ALA 3.0 21.7 + - - -
220H ILE* 3.5 8.2 - - + +
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Residues in contact with LEU 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H CYS* 3.9 13.9 - - + +
20H ASN* 3.9 21.8 - - - -
21H GLN 3.6 26.5 - - - +
28H TRP* 3.1 37.5 - - + -
51H VAL* 4.3 14.1 - - + -
193H VAL* 4.8 1.1 - - + -
198H PRO* 3.1 23.3 - - + +
199H LEU* 3.2 9.9 + - + +
201H ALA* 1.3 74.9 - - - +
203H TYR* 1.3 64.4 + - - +
205H ALA* 3.1 9.3 + - - +
220H ILE* 3.7 31.0 - - + +
222H PRO* 4.2 10.3 - - + -
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Residues in contact with TYR 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3126D EDO 3.5 27.9 + - - -
18H PHE* 4.3 12.8 - + + -
19H CYS* 4.0 20.7 - - + +
97H ARG* 4.5 2.9 + - - -
98H ASP* 2.6 34.4 + - + -
101H TYR* 3.8 23.3 - + - -
102H LEU* 3.7 23.8 - - + -
105H LEU* 4.6 7.2 - - + -
199H LEU 3.1 12.4 + - - +
200H THR 3.2 7.6 + - - +
202H LEU* 1.3 76.5 - - - +
204H VAL* 1.3 59.3 + - - +
206H ASN* 2.9 36.2 + - + +
207H LEU* 3.2 27.2 + - + +
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Residues in contact with VAL 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H LEU* 4.4 12.8 - - + -
95H ILE* 4.6 14.6 - - + -
102H LEU* 4.4 15.7 - - + -
172H LEU* 3.6 16.2 - - + -
175H GLN* 3.4 34.3 - - - +
179H LEU* 4.8 3.4 - - + -
200H THR 3.0 17.9 + - - +
201H ALA 3.5 2.7 - - - +
202H LEU 3.2 0.4 - - - -
203H TYR* 1.3 75.8 - - - +
205H ALA* 1.3 58.6 + - - +
207H LEU* 2.9 10.9 + - - +
208H ILE* 2.8 40.8 + - + +
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Residues in contact with ALA 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 3.2 48.2 - - + -
28H TRP* 3.8 3.4 - - + -
201H ALA 3.0 7.0 + - - +
202H LEU 3.1 12.1 + - - +
204H VAL* 1.3 76.6 - - - +
206H ASN* 1.3 61.8 + - - +
208H ILE* 3.2 13.4 + - + +
209H LYS 3.1 17.8 + - - -
220H ILE* 3.8 19.3 - - + -
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Residues in contact with ASN 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 5.8 1.8 - - - +
19H CYS* 3.9 21.7 - - - -
23H PHE* 4.8 0.6 - - - -
28H TRP* 3.0 25.8 + - - -
202H LEU 3.4 2.4 + - - -
203H TYR* 2.9 27.9 + - + +
205H ALA* 1.3 80.0 - - - +
207H LEU* 1.3 58.0 + - + +
209H LYS* 3.3 16.4 + - - +
210H GLU* 2.9 26.9 + - - +
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Residues in contact with LEU 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LEU* 3.8 13.2 - - + -
94H LEU* 3.4 16.9 - - + +
95H ILE* 3.9 35.0 - - + -
97H ARG* 3.7 4.9 - - - +
98H ASP* 3.6 17.9 - - - +
102H LEU* 4.3 5.8 - - + -
203H TYR* 3.7 36.3 - - + +
204H VAL* 2.9 10.7 + - - +
206H ASN* 1.3 78.4 - - + +
208H ILE* 1.3 53.7 + - - +
210H GLU* 3.6 21.8 - - - +
211H ALA* 2.7 36.2 + - - +
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Residues in contact with ILE 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 5.0 2.0 - - + -
26H ASN* 4.9 7.9 - - - +
91H LEU* 3.9 25.1 - - + -
175H GLN* 5.0 2.2 - - - +
179H LEU* 3.8 28.7 - - + -
183H LEU* 5.5 0.9 - - + -
204H VAL* 2.8 22.9 + - + +
205H ALA* 3.2 15.0 + - + +
207H LEU* 1.3 74.5 - - - +
209H LYS* 1.3 64.2 + - - +
211H ALA 3.3 7.6 + - - -
212H GLY 3.4 3.1 + - - -
213H PHE* 3.4 44.5 + - + -
218H VAL* 3.9 35.9 - - + +
220H ILE* 5.4 0.2 - - + -
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Residues in contact with LYS 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 4.2 6.7 - - + -
26H ASN* 3.2 57.3 + - + +
27H GLU* 5.2 3.8 - - - +
28H TRP* 5.7 6.0 - - - +
205H ALA 3.1 12.1 + - - +
206H ASN* 3.3 18.8 + - - +
208H ILE* 1.3 77.6 - - - +
210H GLU* 1.3 63.8 + - - +
212H GLY* 3.0 15.6 + - - -
213H PHE 4.3 0.6 + - - -
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Residues in contact with GLU 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LYS* 4.1 16.8 - - - +
90H ARG* 4.6 7.4 + - - +
94H LEU* 3.7 15.6 - - + +
97H ARG* 2.8 45.5 + - - -
206H ASN 2.9 16.0 + - - +
207H LEU* 3.2 14.2 + - - +
209H LYS* 1.3 78.6 - - - +
211H ALA* 1.3 61.7 - - - +
212H GLY* 3.3 1.7 + - - -
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Residues in contact with ALA 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H LEU* 3.4 17.2 - - - +
90H ARG* 3.8 22.7 - - + +
91H LEU* 4.0 12.3 - - + +
94H LEU* 3.8 14.4 - - + -
207H LEU 2.7 20.5 + - - +
208H ILE 3.5 7.0 - - - +
209H LYS 3.2 0.2 - - - -
210H GLU* 1.3 73.3 - - - +
212H GLY* 1.3 57.6 + - - +
213H PHE* 3.7 20.0 - - + -
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Residues in contact with GLY 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H MET* 5.5 0.7 - - - +
87H LEU* 4.1 12.6 - - - +
209H LYS 3.0 12.6 + - - -
210H GLU 3.2 1.5 - - - -
211H ALA* 1.3 79.6 - - - +
213H PHE* 1.3 67.3 + - - +
214H PRO* 3.4 7.4 - - - +
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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
------------------------------------------------------------
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