Contacts of the helix formed by residues 198 - 212 (chain G) in PDB entry 3SZ9
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G PHE* 4.1 6.5 - - + -
39G THR* 3.5 14.6 - - - +
51G VAL* 4.0 36.6 - - + -
109G ASP* 3.0 13.7 - - - +
193G VAL* 4.0 19.3 - - + +
194G ALA 3.2 9.2 - - - +
195G GLU 3.7 10.5 - - - +
196G GLN 3.6 1.1 - - - -
197G THR* 1.3 90.7 - - - +
199G LEU* 1.3 63.4 + - + +
200G THR 3.6 0.4 - - - -
201G ALA* 3.5 7.3 + - - +
202G LEU* 3.3 25.8 + - + +
222G PRO* 4.4 6.1 - - + -
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Residues in contact with LEU 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 3.9 16.8 - - + -
19G CYS 3.9 20.6 - - - +
20G ASN* 4.7 0.4 - - + -
39G THR* 3.8 13.2 - - + -
48G ILE* 3.8 28.9 - - + -
49G CYS* 3.9 19.3 - - - -
51G VAL* 3.9 19.3 - - + -
105G LEU* 4.2 23.0 - - + +
109G ASP* 3.3 22.1 + - + +
197G THR 3.4 0.2 - - - -
198G PRO* 1.3 77.7 - - + +
200G THR* 1.3 66.5 + - - +
202G LEU* 3.3 7.3 + - + +
203G TYR* 3.1 21.8 + - - +
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Residues in contact with THR 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 3.8 12.3 - - + +
105G LEU* 3.7 21.5 - - + +
106G GLU* 2.6 55.2 + - + +
109G ASP* 4.9 2.8 + - + -
171G PRO* 3.8 11.1 - - - +
172G LEU* 3.5 21.2 - - + +
197G THR* 4.8 1.8 + - - -
198G PRO 3.6 0.4 - - - -
199G LEU* 1.3 76.5 - - - +
201G ALA* 1.3 62.0 + - - +
203G TYR* 3.4 4.0 + - - +
204G VAL* 3.1 25.6 + - - +
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Residues in contact with ALA 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G ILE* 5.2 0.2 - - + -
171G PRO* 5.2 5.6 - - + +
172G LEU* 4.8 0.2 - - - -
175G GLN* 3.2 41.7 + - + +
193G VAL* 3.4 33.4 - - + -
197G THR 5.2 2.2 + - - +
198G PRO 3.5 5.5 + - - +
199G LEU 3.3 0.4 - - - -
200G THR* 1.3 80.0 + - - +
202G LEU* 1.3 60.7 + - - +
204G VAL 3.2 1.0 + - - -
205G ALA 3.0 22.2 + - - -
220G ILE* 3.7 7.0 - - + +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G CYS* 3.7 27.6 - - + +
20G ASN* 3.9 12.1 - - - -
21G GLN 3.3 26.5 - - - +
28G TRP* 3.0 33.2 - - + -
51G VAL* 4.2 15.0 - - + -
193G VAL* 4.9 0.9 - - + -
198G PRO* 3.3 22.2 + - + +
199G LEU* 3.3 8.4 + - + +
201G ALA* 1.3 75.7 - - - +
203G TYR* 1.3 63.6 + - - +
205G ALA* 3.3 8.7 - - - +
206G ASN 3.6 0.3 + - - -
220G ILE* 3.8 30.5 - - + +
222G PRO* 4.0 11.2 - - + -
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Residues in contact with TYR 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 4.3 18.2 - + + -
19G CYS* 4.0 21.4 - - + +
97G ARG* 4.7 1.2 + - - -
98G ASP* 2.5 34.9 + - + -
101G TYR* 3.8 33.4 - + - -
102G LEU* 3.7 21.1 - - + -
105G LEU* 4.6 7.2 - - + -
199G LEU 3.1 12.4 + - - +
200G THR 3.7 8.1 - - - +
201G ALA 3.3 0.2 - - - -
202G LEU* 1.3 75.2 - - - +
204G VAL* 1.3 64.0 + - - +
206G ASN* 3.0 26.3 + - + +
207G LEU* 3.3 27.8 + - + +
6921G EDO 3.1 18.8 - - - -
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Residues in contact with VAL 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 4.4 16.4 - - + -
95G ILE* 4.4 17.7 - - + -
102G LEU* 4.2 18.8 - - + -
172G LEU* 3.6 15.5 - - + -
175G GLN* 3.3 32.5 - - - +
179G LEU* 5.1 1.6 - - + -
200G THR 3.1 17.6 + - - +
201G ALA 3.2 3.5 + - - +
203G TYR* 1.3 76.3 - - - +
205G ALA* 1.3 56.8 + - - +
207G LEU* 2.9 9.4 + - + +
208G ILE* 2.8 38.4 + - + +
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Residues in contact with ALA 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 3.3 47.9 - - + -
28G TRP* 3.9 3.1 - - + -
201G ALA 3.0 12.1 + - - +
202G LEU* 3.3 12.8 - - - +
203G TYR 3.1 0.2 - - - -
204G VAL* 1.3 76.5 - - - +
206G ASN* 1.3 60.3 + - - +
208G ILE* 3.2 13.1 + - + +
209G LYS 3.0 19.6 + - - -
220G ILE* 3.9 13.0 - - + -
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Residues in contact with ASN 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 5.2 4.0 - - - +
19G CYS* 3.5 25.9 - - - -
23G PHE* 4.8 2.1 - - - -
28G TRP* 3.0 25.3 + - - +
202G LEU 3.6 2.4 + - - -
203G TYR* 3.0 22.3 + - + +
205G ALA* 1.3 77.2 - - - +
207G LEU* 1.3 62.9 + - + +
209G LYS* 3.4 14.9 + - - +
210G GLU* 2.9 27.2 + - - +
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Residues in contact with LEU 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 3.9 13.2 - - + -
94G LEU* 3.4 12.2 - - + +
95G ILE* 3.8 36.8 - - + +
97G ARG* 3.6 5.4 - - - +
98G ASP* 3.4 22.2 - - - +
102G LEU* 4.3 4.9 - - + -
203G TYR* 3.7 35.4 - - + +
204G VAL* 2.9 11.6 + - - +
206G ASN* 1.3 76.8 - - + +
208G ILE* 1.3 54.3 + - - +
210G GLU* 3.6 22.7 - - - +
211G ALA* 2.7 36.4 + - - +
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Residues in contact with ILE 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 4.7 2.5 - - + -
26G ASN* 4.7 9.4 - - - +
91G LEU* 3.9 23.6 - - + -
175G GLN* 5.0 2.5 - - - +
179G LEU* 3.8 28.7 - - + -
183G LEU* 5.5 0.9 - - + -
204G VAL* 2.8 21.1 + - + +
205G ALA* 3.2 17.0 + - - +
207G LEU* 1.3 73.6 - - - +
209G LYS* 1.3 66.3 + - - +
211G ALA 3.3 7.4 + - - -
212G GLY 3.4 8.0 + - - -
213G PHE* 3.4 36.6 + - + -
218G VAL* 3.8 35.7 - - + +
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Residues in contact with LYS 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 4.2 5.8 - - + -
26G ASN* 3.4 53.2 + - + +
27G GLU* 5.2 4.8 - - - +
28G TRP* 5.9 2.9 - - + +
205G ALA 3.0 12.2 + - - +
206G ASN* 3.6 17.9 - - - +
208G ILE* 1.3 77.8 - - - +
210G GLU* 1.3 63.2 - - - +
212G GLY* 3.1 14.9 + - - -
213G PHE 4.4 1.1 + - - +
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Residues in contact with GLU 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ARG* 4.9 9.4 + - - +
94G LEU* 3.9 13.4 - - + +
97G ARG* 2.8 43.7 + - - -
206G ASN 2.9 16.2 + - - +
207G LEU* 3.2 15.8 + - - +
209G LYS* 1.3 78.5 - - - +
211G ALA* 1.3 62.2 + - - +
212G GLY* 3.3 1.7 + - - -
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Residues in contact with ALA 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G LEU* 3.2 18.8 - - - +
90G ARG* 3.8 22.2 - - + +
91G LEU* 4.0 15.5 - - + +
94G LEU* 3.6 14.8 - - + +
207G LEU 2.7 21.9 + - - +
208G ILE 3.6 6.1 - - - +
209G LYS 3.2 0.4 - - - -
210G GLU* 1.3 74.2 - - - +
212G GLY* 1.3 56.3 + - - +
213G PHE* 3.7 15.9 - - + -
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Residues in contact with GLY 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G MET* 5.4 1.0 - - - +
87G LEU* 4.1 13.7 - - - +
208G ILE 3.4 0.2 + - - -
209G LYS 3.1 11.7 + - - -
210G GLU 3.2 1.7 - - - -
211G ALA* 1.3 78.4 - - - +
213G PHE* 1.3 67.1 + - - +
214G 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
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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