Contacts of the helix formed by residues 214 - 226 (chain C) in PDB entry 5W5T
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 THR 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C ILE* 4.2 15.3 - - + -
123C GLU* 5.6 4.3 - - + -
126C ALA* 5.9 0.7 - - - -
127C PRO* 2.9 31.9 + - + +
128C GLU 2.9 15.4 + - - -
129C TYR 3.4 3.8 + - - -
130C MET* 3.3 31.4 - - + +
212C PHE 3.8 1.0 + - - -
213C HIS* 1.3 71.7 - - - +
215C LYS* 1.3 57.8 + - - +
217C LEU* 3.2 1.8 + - - +
218C MET* 2.9 51.5 + - + +
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Residues in contact with LYS 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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213C HIS* 3.3 4.6 - - + +
214C THR* 1.3 78.5 - - - +
216C PHE* 1.3 61.9 + - - +
218C MET* 3.5 7.1 + - - +
219C GLU* 3.1 43.1 + - + +
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Residues in contact with PHE 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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156C ASP* 3.4 60.3 - - + +
212C PHE* 3.8 11.0 - + - -
213C HIS* 3.3 20.0 + - + +
215C LYS* 1.3 76.4 - - - +
217C LEU* 1.3 62.5 + - - +
219C GLU* 3.2 20.3 - - + +
220C ALA* 2.9 32.3 + - + +
223C ARG* 5.3 6.5 - - - -
242C ILE* 3.6 31.6 - - + -
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Residues in contact with LEU 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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115C VAL* 4.4 6.1 - - + -
130C MET* 3.7 33.2 - - + -
132C ILE* 4.0 14.8 - - + -
212C PHE* 3.5 45.1 - - + -
213C HIS 3.1 16.8 + - - +
214C THR* 3.2 4.9 + - - +
216C PHE* 1.3 78.1 - - - +
218C MET* 1.3 72.5 + - + +
220C ALA* 3.3 4.2 + - + +
221C LEU* 2.8 59.4 + - + +
234C PHE* 3.7 7.0 - - + -
238C ILE* 5.0 0.7 - - + -
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Residues in contact with MET 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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115C VAL* 4.1 14.6 - - + -
119C ILE* 3.7 32.3 - - + -
122C ILE* 4.4 13.7 - - + -
123C GLU* 3.9 17.3 - - + +
130C MET* 4.4 2.0 - - + -
214C THR* 2.9 43.4 + - + +
215C LYS* 3.9 6.1 - - - +
217C LEU* 1.3 100.8 - - + +
219C GLU* 1.3 57.2 + - - +
221C LEU* 3.3 4.2 + - + +
222C ARG* 2.9 57.1 + - - +
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Residues in contact with GLU 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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215C LYS* 3.1 47.5 + - + +
216C PHE* 3.2 23.2 - - + +
218C MET* 1.3 75.6 - - - +
220C ALA* 1.3 63.0 + - - +
222C ARG* 3.2 9.1 + - - +
223C ARG* 3.0 25.5 + - - +
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Residues in contact with ALA 220 (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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216C PHE* 2.9 32.0 + - + +
217C LEU* 3.7 9.0 - - + +
219C GLU* 1.3 72.2 - - - +
221C LEU* 1.3 60.2 + - + +
223C ARG* 3.2 31.6 + - - +
224C ASP* 2.9 29.5 + - - +
238C ILE* 4.5 22.4 - - + +
242C ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 221 (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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112C ALA* 2.9 31.6 - - + +
115C VAL* 3.3 17.3 - - + -
116C TYR* 3.1 42.3 - - + +
119C ILE* 5.0 2.7 - - + -
217C LEU* 2.8 52.2 + - + +
218C MET* 3.8 6.7 - - + +
220C ALA* 1.3 77.5 - - - +
222C ARG* 1.3 57.9 + - - +
224C ASP* 3.8 4.8 - - + +
225C ALA* 3.2 20.6 + - - +
232C ARG* 4.6 0.7 + - - -
234C PHE* 4.1 4.0 - - + -
238C ILE* 3.5 20.4 - - + -
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Residues in contact with ARG 222 (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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116C TYR* 4.1 19.8 - - + -
119C ILE* 3.4 29.8 - - + +
123C GLU* 3.3 32.9 + - - -
218C MET* 2.9 34.5 + - - +
219C GLU* 3.2 6.2 + - - +
221C LEU* 1.3 75.8 - - - +
223C ARG* 1.3 64.9 + - - +
225C ALA* 3.7 1.9 + - - +
226C ALA* 3.6 20.8 + - - +
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Residues in contact with ARG 223 (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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216C PHE* 5.3 6.9 - - - -
219C GLU* 3.0 14.8 + - - +
220C ALA* 3.6 33.5 + - - +
222C ARG* 1.3 79.1 - - - +
224C ASP* 1.3 62.7 + - - +
226C ALA* 3.5 5.5 + - - +
227C ASP* 3.5 20.6 + - + +
238C ILE* 5.4 3.0 + - - +
241C TYR* 3.4 54.9 + - - +
242C ILE* 4.7 9.5 - - - +
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Residues in contact with ASP 224 (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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112C ALA* 3.9 6.8 - - - +
220C ALA 2.9 16.4 + - - +
221C LEU* 3.8 7.9 - - - +
222C ARG 3.3 0.2 - - - -
223C ARG* 1.3 79.2 - - - +
225C ALA* 1.3 61.6 + - - +
227C ASP* 3.1 25.5 + - - +
230C SER* 2.3 26.5 + - - -
232C ARG* 2.7 41.8 + - - -
237C ASP* 3.7 11.7 - - - +
238C ILE* 4.4 19.0 + - + +
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Residues in contact with ALA 225 (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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116C TYR* 3.6 30.3 - - + +
221C LEU 3.2 13.5 + - - +
222C ARG 4.1 3.1 - - - +
223C ARG 3.4 0.4 - - - -
224C ASP* 1.3 80.9 + - - +
226C ALA* 1.3 59.2 + - - +
227C ASP 3.2 4.0 + - - +
228C PRO* 5.6 0.7 - - - +
232C ARG* 3.4 35.5 + - - +
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Residues in contact with ALA 226 (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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222C ARG 3.6 13.1 + - - +
223C ARG* 3.5 5.5 + - - +
224C ASP 3.2 0.6 - - - -
225C ALA* 1.3 78.4 - - + +
227C ASP* 1.3 57.9 + - - +
228C PRO* 3.2 14.2 - - - +
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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