Contacts of the helix formed by residues 209 - 220 (chain L) in PDB entry 5PRC
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 ALA 209 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H LYS* 4.7 10.9 - - - +
176H SER* 4.1 8.3 - - - -
177H GLU* 4.0 33.2 - - + +
208L THR* 1.3 73.1 - - - +
210L GLU* 1.3 69.2 + - - +
211L HIS 3.3 0.7 + - - -
212L GLU* 3.3 26.9 + - - +
213L ASN* 3.4 17.5 + - - +
233M ILE* 5.1 1.8 - - - +
234M GLU* 4.8 7.9 + - - +
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Residues in contact with GLU 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ALA 5.4 0.2 - - - +
127H THR* 3.5 6.1 - - - -
128H VAL* 3.1 33.4 + - + +
133H LYS* 5.2 1.2 - - - -
175H ARG 4.4 1.6 - - - +
176H SER* 2.8 53.2 + - - +
208L THR* 3.2 17.0 + - - +
209L ALA* 1.3 74.6 + - - +
211L HIS* 1.3 57.3 + - - +
213L ASN* 3.8 6.6 + - - +
214L GLN* 3.1 28.1 + - - +
17M ILE* 3.9 21.3 - - + +
19M VAL* 3.4 22.9 - - + +
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Residues in contact with HIS 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H VAL* 4.0 15.2 - - + +
197L VAL* 5.0 0.9 - - + -
207L LYS* 3.7 38.9 - - + +
208L THR* 2.9 36.5 + - + +
210L GLU* 1.3 77.5 - - - +
212L GLU* 1.3 57.5 + - - +
213L ASN 3.3 0.2 - - - -
214L GLN* 3.6 6.3 - - - +
215L TYR* 2.8 33.6 + - - +
19M VAL* 3.6 26.7 - - + +
20M SER 5.8 0.2 + - - -
138M LEU* 3.2 34.0 + - + +
140M LEU* 4.1 12.5 - - + +
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Residues in contact with GLU 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L HIS* 5.8 0.5 - - - -
193L LEU* 3.6 32.6 - - + +
194L ILE* 3.9 17.3 - - - +
197L VAL* 3.7 22.0 - - + +
208L THR 4.0 5.6 - - - +
209L ALA* 3.5 17.1 - - - +
211L HIS* 1.3 79.7 - - - +
213L ASN* 1.3 64.7 + - - +
215L TYR* 3.3 9.7 + - - +
216L PHE* 3.5 18.4 + - - +
223L SER* 4.5 0.2 + - - -
226L ALA* 4.6 11.2 - - - +
502L ATZ 3.6 21.9 - - + +
232M GLU 5.6 1.2 + - - -
233M ILE* 3.2 28.0 - - - +
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Residues in contact with ASN 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H SER 4.1 17.0 + - - -
177H GLU* 4.6 13.7 + - - +
209L ALA 3.4 12.2 + - - +
210L GLU* 3.9 8.9 - - - +
211L HIS 3.3 0.2 - - - -
212L GLU* 1.3 78.9 - - - +
214L GLN* 1.3 63.0 + - - +
216L PHE 3.4 0.3 + - - -
217L ARG* 3.1 59.2 + - - +
223L SER* 2.7 33.3 + - - +
225L GLY* 4.0 8.4 - - - -
502L ATZ 3.6 10.5 - - - +
43M ASP* 5.0 6.2 + - - -
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Residues in contact with GLN 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L GLU 3.1 20.7 + - - +
211L HIS* 3.6 5.4 - - - +
212L GLU 3.3 0.2 - - - -
213L ASN* 1.3 77.6 - - - +
215L TYR* 1.3 62.5 + - - +
217L ARG* 3.5 18.2 + - - +
218L ASP* 2.9 53.7 + - - +
17M ILE* 3.9 8.7 + - - +
18M THR* 3.7 12.4 + - - +
19M VAL* 3.3 48.5 - - + +
28M ARG* 3.5 13.2 + - - -
48M PRO* 5.8 2.4 - - - +
138M LEU* 3.9 14.1 - - + -
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Residues in contact with TYR 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L LEU* 4.0 13.0 - - + -
211L HIS 2.8 20.2 + - - +
212L GLU 3.3 5.8 + - - +
214L GLN* 1.3 74.8 - - - +
216L PHE* 1.3 84.0 + + - +
218L ASP* 3.3 2.4 + - - +
219L VAL* 2.9 43.8 + - + +
131M VAL* 2.8 38.9 + - - +
134M ARG* 3.7 14.1 - - + -
135M ALA* 3.5 32.3 - - + -
138M LEU* 3.6 8.5 - - + +
140M LEU* 3.8 26.7 - - + -
144M ILE* 3.7 27.0 - - + +
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Residues in contact with PHE 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L LEU* 4.1 13.5 - - + -
193L LEU* 4.1 17.0 - - + -
212L GLU 3.5 6.8 + - - -
213L ASN 3.4 1.8 + - - -
214L GLN 3.3 0.4 - - - -
215L TYR* 1.3 96.7 - + - +
217L ARG* 1.3 61.6 + - - +
218L ASP 3.1 1.6 - - - -
219L VAL* 4.1 6.3 - - + +
220L VAL* 2.8 34.7 + - + +
221L GLY 3.1 4.2 + - - -
222L TYR 3.3 16.4 - - - +
223L SER* 3.9 6.5 - - - -
502L ATZ 3.4 73.4 - + + +
144M ILE* 3.8 21.1 - - + -
401M BPB 4.2 14.6 - - - -
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Residues in contact with ARG 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H HIS* 6.0 3.2 - - - -
213L ASN* 3.1 47.9 + - - +
214L GLN* 3.8 20.8 - - - +
216L PHE* 1.3 74.7 - - - +
218L ASP* 1.3 61.3 + - - +
221L GLY* 2.9 24.7 + - - +
222L TYR* 3.8 12.0 + - - +
223L SER* 4.3 15.0 + - - +
17M ILE* 4.3 21.2 + - - +
43M ASP* 3.0 33.9 + - - -
45M GLN* 3.6 42.9 + - - +
47M GLY 4.3 10.3 - - - +
48M PRO* 3.2 19.1 - - + +
49M ILE* 3.7 2.1 - - - +
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Residues in contact with ASP 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L GLN* 2.9 30.5 + - - +
215L TYR* 3.3 5.8 - - - +
217L ARG* 1.3 82.1 - - - +
219L VAL* 1.3 52.9 + - - +
28M ARG* 2.8 36.2 + - - +
48M PRO 5.6 0.5 - - - +
49M ILE* 3.6 1.0 - - - +
50M TYR* 3.3 19.6 + - + +
130M ARG* 2.7 27.8 + - - -
134M ARG* 2.9 44.1 + - - -
138M LEU* 3.8 8.7 - - - +
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Residues in contact with VAL 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L TYR* 2.9 50.3 + - + +
216L PHE* 3.2 7.1 + - + +
218L ASP* 1.3 77.9 - - - +
220L VAL* 1.3 70.7 + - + +
49M ILE* 4.3 1.4 - - - +
127M TRP* 3.4 23.7 - - + -
130M ARG* 2.8 35.8 + - - +
131M VAL* 4.4 13.5 - - + -
134M ARG* 3.9 15.7 - - + -
401M BPB 4.1 11.7 - - - +
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Residues in contact with VAL 220 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216L PHE* 2.8 18.9 + - + +
219L VAL* 1.3 84.7 - - + +
221L GLY* 1.3 60.4 + - - +
222L TYR* 3.3 22.1 + - + +
502L ATZ 3.7 20.0 - - + -
49M ILE* 3.5 14.0 - - - +
127M TRP* 4.7 5.6 - - + -
401M BPB 3.5 33.9 - - + +
805M BCB 3.5 44.7 - - + +
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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