Contacts of the helix formed by residues 211 - 219 (chain I) in PDB entry 5XVO
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 PHE 211 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I LEU* 3.8 37.2 - - + -
73I PRO* 4.5 2.5 - - + -
184I LEU* 4.1 24.0 - - + -
188I ALA* 3.8 24.7 - - + -
198I THR* 3.3 19.1 - - - -
209I ASN* 3.0 18.5 + - - +
210I ASP* 1.3 89.5 - - + +
212I ASN* 1.3 65.7 + - - +
213I LEU 3.1 2.9 - - - -
214I ALA* 2.9 23.0 + - + -
215I SER* 3.0 11.6 + - - -
81J TYR* 3.4 36.1 - + - -
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Residues in contact with ASN 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I THR 3.1 3.0 + - - -
199I GLN 3.2 21.6 + - - +
200I LEU* 4.9 1.8 - - - +
201I GLY* 3.6 16.9 - - - +
203I LYS 5.9 2.2 - - - +
204I HIS* 5.1 9.1 - - - +
208I PHE* 3.7 31.8 - - - +
209I ASN* 3.5 27.8 + - - +
210I ASP 3.8 0.6 - - - -
211I PHE* 1.3 76.7 - - - +
213I LEU* 1.3 58.1 + - - +
215I SER* 3.1 11.5 + - - -
216I ASP* 3.0 31.1 + - - +
87J SER* 4.6 1.6 + - - -
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Residues in contact with LEU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I GLN* 3.8 14.1 - - - +
96I TRP* 4.2 14.8 - - + -
191I LEU* 3.7 29.8 - - + +
196I CYS* 4.4 2.0 - - + -
197I PHE 3.5 18.2 - - - +
198I THR* 3.0 18.4 + - - +
200I LEU 3.8 8.5 - - - +
201I GLY* 3.8 11.1 - - - -
202I LEU* 3.9 36.3 - - + -
212I ASN* 1.3 78.5 - - - +
214I ALA* 1.3 61.8 + - - +
216I ASP* 3.4 5.4 + - + +
217I LEU* 3.2 29.5 + - + +
276I LEU* 5.4 1.6 - - + -
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Residues in contact with ALA 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I LEU* 3.6 19.1 - - + +
187I PHE* 4.2 5.6 - - + +
188I ALA* 3.8 30.3 - - - +
191I LEU* 3.6 11.9 - - + +
198I THR* 4.3 2.6 + - - -
211I PHE* 2.9 19.7 + - + +
213I LEU* 1.3 78.1 - - - +
215I SER* 1.3 63.8 + - - +
217I LEU* 3.2 3.0 + - - +
218I MET* 3.0 24.9 + - - +
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Residues in contact with SER 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I LEU* 3.6 12.7 - - - +
209I ASN* 3.7 13.7 + - - -
211I PHE 3.0 13.6 + - - -
212I ASN* 3.1 11.6 + - - -
214I ALA* 1.3 75.4 - - - +
216I ASP* 1.3 66.0 + - - +
218I MET* 3.1 26.6 - - - +
219I GLU* 3.3 20.4 - - - +
222I ARG* 4.9 3.8 - - - -
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Residues in contact with ASP 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I TRP* 3.7 29.2 + - + -
108I ILE* 3.6 13.0 - - + +
201I GLY* 3.4 7.6 - - - -
202I LEU* 2.7 44.3 + - + -
203I LYS* 3.8 5.6 + - - +
212I ASN* 3.0 13.6 + - - +
213I LEU* 3.5 9.2 - - + +
214I ALA 3.2 0.2 - - - -
215I SER* 1.3 78.4 - - - +
217I LEU* 1.3 62.2 + - + +
219I GLU* 3.2 26.4 + - - +
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Residues in contact with LEU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ILE* 4.2 12.5 - - + +
187I PHE* 4.1 14.0 - - + -
191I LEU* 3.9 19.3 - - + -
202I LEU* 4.9 3.4 - - + -
213I LEU* 3.2 26.3 + - + +
214I ALA* 3.2 4.5 + - - +
216I ASP* 1.3 81.5 - - + +
218I MET* 1.3 61.0 + - - +
219I GLU 3.2 1.8 + - - -
220I PRO* 3.4 11.8 - - - +
221I PHE* 4.1 3.5 - - - -
268I TYR* 3.6 18.0 - - + -
269I THR* 3.7 42.4 - - + +
272I VAL* 3.7 34.8 - - + -
273I VAL* 5.5 0.7 - - + -
276I LEU* 5.6 1.1 - - + -
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Residues in contact with MET 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180I TYR* 3.5 27.4 - - + +
183I LEU* 3.8 16.2 - - + +
184I LEU* 3.8 34.8 - - - -
187I PHE* 3.7 28.9 - - + -
214I ALA 3.0 11.1 + - - +
215I SER* 3.1 20.9 - - - +
217I LEU* 1.3 77.0 - - - +
219I GLU* 1.3 63.4 + - - +
220I PRO* 3.4 2.2 - - - -
221I PHE* 2.9 20.1 + - - +
222I ARG* 3.5 44.2 + - + +
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Residues in contact with GLU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I TRP* 5.7 4.7 - - - +
108I ILE* 4.1 8.5 - - + -
109I ILE* 4.8 6.9 - - + +
112I LYS* 3.0 52.9 + - + +
148I GLU* 3.5 11.2 - - - +
215I SER* 3.3 12.1 - - - +
216I ASP* 3.2 23.2 - - - +
217I LEU 3.2 0.2 - - - -
218I MET* 1.3 76.8 - - - +
220I PRO* 1.3 70.9 - - + +
221I PHE 3.0 1.6 + - - -
222I ARG* 2.6 46.6 + - - +
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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