Contacts of the helix formed by residues 198 - 212 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F PHE* 4.2 6.7 - - + -
39F THR* 3.6 9.0 - - - +
51F VAL* 3.9 25.1 - - + -
109F ASP* 3.3 10.1 - - - +
193F VAL* 3.8 17.8 - - + +
194F ALA 3.6 9.4 - - - +
195F GLU 3.4 15.5 - - - +
196F GLN 3.6 1.3 - - - -
197F THR* 1.3 91.9 - - - +
199F LEU* 1.3 63.6 + - + +
200F THR 3.5 1.1 + - - -
201F ALA* 3.5 6.4 + - - +
202F LEU* 3.3 28.9 + - + +
222F PRO* 4.3 15.5 - - + -
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 3.9 22.7 - - + -
19F CYS 3.9 11.6 - - - +
20F ASN* 4.7 0.4 - - + -
39F THR* 3.8 19.3 - - + -
48F ILE* 3.9 23.1 - - + -
49F CYS* 3.9 19.3 - - - -
51F VAL* 4.0 17.0 - - + -
105F LEU* 4.1 25.2 - - + +
109F ASP* 3.3 25.0 + - - +
197F THR 3.4 0.4 - - - -
198F PRO* 1.3 80.2 - - + +
200F THR* 1.3 64.1 + - - +
202F LEU* 3.2 7.5 + - + +
203F TYR* 3.0 21.1 + - - +
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Residues in contact with THR 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 3.9 10.9 - - + +
105F LEU* 3.6 23.8 - - + +
106F GLU* 2.7 53.0 + - + +
109F ASP* 4.9 2.4 + - + -
171F PRO* 3.8 10.4 - - - +
172F LEU* 3.4 21.9 + - + +
197F THR 4.8 1.2 + - - -
199F LEU* 1.3 76.0 - - - +
201F ALA* 1.3 59.2 + - - +
203F TYR* 3.1 3.5 + - - +
204F VAL* 2.9 31.5 + - - +
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Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ILE* 5.3 0.4 - - + -
171F PRO* 5.3 5.6 - - + +
172F LEU* 4.5 0.6 - - - +
175F GLN* 3.2 40.9 + - + +
193F VAL* 3.4 33.9 - - + -
197F THR 5.2 2.0 + - - +
198F PRO 3.5 6.6 + - - +
199F LEU 3.3 0.6 - - - -
200F THR* 1.3 80.8 + - - +
202F LEU* 1.3 59.4 + - - +
204F VAL 3.3 0.9 + - - -
205F ALA 3.0 20.8 + - - -
220F ILE* 3.5 6.9 - - + +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F CYS* 3.8 22.0 - - - +
20F ASN* 4.0 9.9 - - - -
21F GLN 3.5 26.7 - - - +
28F TRP* 3.1 33.5 - - + -
51F VAL* 4.1 17.9 - - + -
193F VAL* 5.1 1.1 - - + -
198F PRO* 3.3 21.1 + - + +
199F LEU* 3.2 8.9 + - + +
200F THR 3.2 0.6 - - - -
201F ALA* 1.3 74.3 - - - +
203F TYR* 1.3 64.3 + - - +
205F ALA* 3.1 10.4 + - - +
206F ASN 3.3 2.6 + - - -
220F ILE* 3.8 29.8 - - + +
222F PRO* 4.2 11.9 - - + -
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Residues in contact with TYR 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 4.3 13.2 - + + -
19F CYS* 4.0 21.6 - - + +
97F ARG* 4.6 1.7 + - - -
98F ASP* 2.6 36.7 + - + -
101F TYR* 3.8 25.4 - + - -
102F LEU* 3.7 23.3 - - + -
105F LEU* 4.4 9.0 - - + -
199F LEU 3.0 12.1 + - - +
200F THR 3.1 6.9 + - - +
202F LEU* 1.3 75.4 - - - +
204F VAL* 1.3 62.0 + - - +
206F ASN* 3.0 30.5 + - + +
207F LEU* 3.3 26.6 + - + +
6921F EDO 3.4 28.4 + - - -
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Residues in contact with VAL 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.6 6.3 - - + -
95F ILE* 4.4 23.3 - - + -
102F LEU* 4.2 16.8 - - + -
172F LEU* 3.4 25.1 - - + -
175F GLN* 3.3 27.8 - - + +
179F LEU* 5.1 1.8 - - + -
200F THR 2.9 17.3 + - - +
201F ALA 3.5 3.8 - - - +
203F TYR* 1.3 73.7 - - - +
205F ALA* 1.3 66.5 + - - +
207F LEU* 2.9 17.5 + - - +
208F ILE* 2.9 23.8 + - + +
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Residues in contact with ALA 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 3.3 48.2 - - + -
28F TRP* 3.8 3.8 - - + -
201F ALA 3.0 13.2 + - - +
202F LEU* 3.1 12.7 + - - +
204F VAL* 1.3 75.3 - - - +
206F ASN* 1.3 63.1 + - - +
208F ILE* 3.1 23.3 + - + +
209F LYS 3.1 10.4 + - - -
220F ILE* 4.1 10.5 - - + -
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Residues in contact with ASN 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 5.7 2.0 - - - +
19F CYS* 3.7 24.0 - - - -
23F PHE* 4.8 2.6 - - - -
28F TRP* 2.9 27.2 + - - -
202F LEU 3.3 2.2 + - - -
203F TYR* 3.0 25.8 + - + +
205F ALA* 1.3 80.7 - - - +
207F LEU* 1.3 57.1 + - + +
209F LYS* 3.5 10.1 + - - +
210F GLU* 3.1 25.0 + - - +
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Residues in contact with LEU 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 3.8 13.0 - - + +
94F LEU* 3.3 17.6 - - + +
95F ILE* 3.8 38.4 - - + +
97F ARG* 3.7 16.8 - - - +
98F ASP* 3.5 19.1 - - - +
102F LEU* 4.3 6.1 - - + -
203F TYR* 3.8 35.0 - - + +
204F VAL* 2.9 11.2 + - - +
206F ASN* 1.3 76.9 - - + +
208F ILE* 1.3 55.3 + - - +
210F GLU* 3.7 11.4 - - - +
211F ALA* 2.7 31.7 + - - +
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Residues in contact with ILE 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 5.0 2.2 - - + -
26F ASN* 4.9 7.9 - - - +
91F LEU* 3.9 24.0 - - + -
175F GLN* 4.9 2.7 - - - +
179F LEU* 3.8 28.7 - - + -
183F LEU* 5.7 0.7 - - + -
204F VAL* 2.9 22.6 + - + +
205F ALA* 3.1 17.9 + - + +
207F LEU* 1.3 74.5 - - - +
209F LYS* 1.3 66.7 + - - +
211F ALA 3.4 3.8 + - - -
213F PHE* 3.4 48.1 + - + -
218F VAL* 3.8 34.8 - - + +
220F ILE* 5.2 0.2 - - + -
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Residues in contact with LYS 209 (chain F).
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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23F PHE* 4.2 8.2 - - + -
26F ASN* 3.5 47.1 + - + +
27F GLU* 3.5 22.3 + - - -
28F TRP* 6.3 0.4 - - - +
205F ALA 3.1 11.7 + - - +
206F ASN* 3.7 14.1 - - - +
208F ILE* 1.3 73.5 - - - +
210F GLU* 1.3 67.6 + - - +
212F GLY* 2.9 15.8 + - - -
213F PHE 5.0 0.5 - - - +
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Residues in contact with GLU 210 (chain F).
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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90F ARG* 4.6 10.7 + - - +
94F LEU* 3.5 17.8 - - + +
97F ARG* 2.8 41.6 + - - -
206F ASN 3.1 12.2 + - - +
207F LEU* 3.6 17.1 - - - +
209F LYS* 1.3 82.3 - - - +
211F ALA* 1.3 61.7 + - - +
212F GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F LEU* 3.2 19.3 - - - +
90F ARG* 3.8 16.0 - - + +
91F LEU* 3.9 19.1 - - + +
94F LEU* 3.5 14.1 - - + +
207F LEU 2.7 20.5 + - - +
208F ILE 3.7 7.2 - - - +
209F LYS 3.2 0.4 - - - -
210F GLU* 1.3 71.8 - - - +
212F GLY* 1.3 58.7 + - - +
213F PHE* 3.6 20.9 - - + -
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Residues in contact with GLY 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F MET* 5.5 0.3 - - - +
87F LEU* 4.1 12.2 - - - +
209F LYS 2.9 14.3 + - - -
210F GLU 3.1 1.7 - - - -
211F ALA* 1.3 80.2 - - - +
213F PHE* 1.3 67.2 + - - +
214F 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