Contacts of the helix formed by residues 201 - 221 (chain C) in PDB entry 5F1B
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 ASP 201 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C TYR* 3.0 25.4 + - + +
199C TYR 3.2 1.8 + - - -
200C ASN* 1.3 84.6 - - + +
202C THR* 1.3 66.5 + - - +
203C GLU* 3.3 14.9 + - - +
204C LYS* 2.8 49.5 + - + +
205C LEU 3.1 13.9 + - - -
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Residues in contact with THR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C TYR 4.9 0.2 - - - -
199C TYR 5.4 1.3 + - - +
200C ASN 4.3 0.6 - - - -
201C ASP* 1.3 72.4 + - - +
203C GLU* 1.3 65.8 + - - +
205C LEU* 3.1 11.6 + - + +
206C GLN* 2.9 44.1 + - - +
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.6 19.9 + - - -
86C ASP* 5.2 1.7 - - - +
201C ASP* 3.3 7.6 + - - +
202C THR* 1.3 83.1 + - - +
204C LYS* 1.3 66.3 + - + +
205C LEU 3.5 0.2 + - - -
206C GLN* 3.5 12.9 + - - +
207C ARG* 2.7 50.6 + - - +
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP 6.0 0.2 - - - +
95C ILE* 4.8 1.1 - - + +
198C TYR* 3.4 49.4 - - + +
201C ASP* 2.8 34.0 + - + +
202C THR 3.4 0.2 - - - -
203C GLU* 1.3 78.3 - - + +
205C LEU* 1.3 66.4 + - - +
207C ARG* 3.2 13.5 + - + +
208C ALA* 3.0 18.0 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ASN 5.6 0.2 - - - +
197C ASN* 3.4 23.1 - - - +
198C TYR* 3.8 15.7 - - + +
199C TYR* 5.7 2.5 - - - -
201C ASP 3.1 15.1 + - - +
202C THR* 3.1 16.5 + - + +
204C LYS* 1.3 77.3 - - - +
206C GLN* 1.3 66.8 + - - +
208C ALA* 3.1 8.2 + - + +
209C GLN* 2.8 62.7 + - + +
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Residues in contact with GLN 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.3 39.1 + - + +
202C THR* 2.9 41.2 + - - +
203C GLU* 3.6 13.9 - - - +
205C LEU* 1.3 91.3 - - - +
207C ARG* 1.3 56.6 + - - +
209C GLN* 3.3 16.3 + - - +
210C ALA* 3.0 27.9 + - - +
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.3 34.9 - - + -
86C ASP* 3.9 6.9 + - - -
88C GLU* 2.5 43.5 + - - +
90C VAL* 3.7 33.2 - - + +
95C ILE* 4.9 4.7 - - + -
203C GLU* 2.7 58.3 + - - +
204C LYS* 3.2 12.9 + - + +
205C LEU 3.2 0.6 - - - -
206C GLN* 1.3 76.5 - - - +
208C ALA* 1.3 64.9 + - - +
210C ALA* 3.4 6.5 + - - +
211C TRP 3.1 18.0 + - - -
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.8 27.5 - - + +
195C VAL* 4.5 8.9 - - + +
196C ASN 4.5 2.2 - - - +
198C TYR* 3.9 18.6 - - + -
204C LYS 3.0 13.2 + - - +
205C LEU* 3.4 13.2 - - + +
207C ARG* 1.3 77.4 - - - +
209C GLN* 1.3 56.4 + - - +
211C TRP* 3.4 3.8 + - - +
212C GLU* 2.9 32.1 + - - +
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Residues in contact with GLN 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 2.8 49.9 + - + +
206C GLN* 3.7 19.7 + - - +
208C ALA* 1.3 73.7 - - + +
210C ALA* 1.3 65.3 + - - +
212C GLU* 3.6 10.3 - - - +
213C LYS* 3.1 23.9 + - - +
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.5 18.6 - - + +
84C SER 4.2 14.4 - - - +
85C TYR* 4.3 14.8 - - + -
90C VAL* 5.3 0.7 - - + -
206C GLN 3.0 14.0 + - - +
207C ARG* 3.6 9.4 - - - +
208C ALA 3.3 0.2 - - - -
209C GLN* 1.3 78.1 - - - +
211C TRP* 1.3 62.2 + - - +
213C LYS* 3.3 15.9 + - - +
214C GLU* 3.4 10.6 + - - +
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Residues in contact with TRP 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 4.3 18.4 - - + -
78C ILE* 3.6 27.8 - - + -
81C ILE* 2.9 39.0 + - + +
83C ALA* 3.6 10.9 - - - +
90C VAL* 3.7 21.8 - - + -
91C THR 3.9 1.3 - - - -
92C LEU* 3.5 41.8 - - + +
95C ILE* 3.7 26.7 - - + -
193C PHE* 5.5 2.2 - + - -
195C VAL* 4.9 0.7 - - + -
207C ARG 3.1 11.5 + - - +
208C ALA 3.7 6.7 - - - +
210C ALA* 1.3 76.0 - - - +
212C GLU* 1.3 70.7 - - + +
214C GLU* 3.2 5.2 + - - +
215C PHE* 3.0 57.4 + + + -
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 2.8 48.2 + - - -
34C GLU* 2.8 32.2 - - - +
195C VAL* 5.4 2.9 - - - +
208C ALA* 2.9 20.7 + - - +
209C GLN* 3.6 11.7 - - - +
210C ALA 3.2 0.4 - - - -
211C TRP* 1.3 86.5 - - + +
213C LYS* 1.3 61.8 + - - +
215C PHE* 3.2 3.5 + - + +
216C ILE* 3.0 46.5 + - + +
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Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C GLN 3.1 17.0 + - - +
210C ALA* 3.7 7.4 - - - +
211C TRP 3.3 0.4 - - - -
212C GLU* 1.3 75.1 - - - +
214C GLU* 1.3 70.9 + - + +
216C ILE* 3.5 10.7 + - - +
217C ASN* 3.3 23.8 + - + +
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 4.0 10.5 - - + +
82C THR 3.8 17.3 - - - +
83C ALA* 3.7 26.2 - - + -
84C SER 5.5 0.2 - - - +
210C ALA 3.4 2.9 + - - +
211C TRP 3.2 9.0 + - - +
213C LYS* 1.3 89.1 - - + +
215C PHE* 1.3 56.5 + - - +
217C ASN* 3.6 9.8 + - - +
218C PHE* 3.0 30.0 + - - +
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Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.7 38.6 - - + -
36C LEU* 3.7 23.3 - - + -
78C ILE* 3.7 35.7 - - + -
81C ILE* 3.9 11.6 - - + +
193C PHE* 4.5 6.5 - + - -
211C TRP* 3.0 39.3 + + + +
212C GLU 3.2 8.5 + - - +
214C GLU* 1.3 75.2 - - - +
216C ILE* 1.3 71.3 + - + +
218C PHE* 3.8 0.2 - - - +
219C VAL* 3.0 44.3 + - + +
231C PHE* 4.1 18.8 - + - -
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 5.6 0.7 - - - +
212C GLU* 3.0 39.9 + - + +
213C LYS* 3.9 8.3 - - - +
215C PHE* 1.3 86.4 - - + +
217C ASN* 1.3 59.6 + - - +
219C VAL* 3.8 0.7 - - - +
220C LYS* 2.8 37.3 + - + +
231C PHE* 4.3 22.6 - - + -
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LYS* 3.3 15.6 + - + +
214C GLU* 3.9 11.2 + - - +
216C ILE* 1.3 78.8 - - - +
218C PHE* 1.3 66.5 + - - +
220C LYS* 3.5 26.4 + - - +
221C ASN* 3.0 30.9 + - - +
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 4.3 7.6 - - + -
77C ALA* 3.7 27.4 - - + -
78C ILE* 4.3 4.9 - - + -
81C ILE* 3.6 30.7 - - + -
214C GLU 3.0 18.3 + - - +
215C PHE 3.8 0.7 - - - +
216C ILE 3.4 0.2 - - - -
217C ASN* 1.3 77.4 - - - +
219C VAL* 1.3 68.8 + - + +
221C ASN 3.2 4.2 + - - -
222C TYR* 3.0 64.9 + + - +
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.5 18.6 - - + -
74C LEU* 4.8 3.6 - - + -
78C ILE* 3.7 22.4 - - + -
215C PHE* 3.0 44.2 + - + +
216C ILE 4.1 1.8 - - - +
218C PHE* 1.3 80.4 - - + +
220C LYS* 1.3 63.6 + - - +
221C ASN 3.4 0.2 + - - -
222C TYR* 3.6 15.6 + - - +
229C ILE* 3.5 36.6 - - + +
231C PHE* 3.9 14.1 - - + -
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Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 2.8 27.7 + - + +
217C ASN* 3.5 20.5 + - - +
219C VAL* 1.3 79.7 - - - +
221C ASN* 1.3 103.6 + - - +
222C TYR 3.5 0.7 + - - -
229C ILE 6.1 0.2 - - - -
231C PHE* 4.7 12.3 - - + -
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Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 3.0 19.4 + - - +
218C PHE 3.2 4.0 + - - -
220C LYS* 1.3 117.4 + - - +
222C TYR* 1.3 63.4 + - - +
223C LYS* 3.3 8.0 + - - +
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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
------------------------------------------------------------
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