Contacts of the helix formed by residues 221 - 232 (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 221 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183I LEU* 3.7 22.3 - - + +
187I PHE* 3.5 32.5 - + + -
217I LEU 4.1 0.7 - - - -
218I MET 2.9 14.5 + - - +
220I PRO* 1.3 87.6 - - + +
222I ARG* 1.3 66.1 + - - +
223I PRO* 3.3 2.2 - - - -
224I LEU* 2.9 25.8 + - + +
261I LEU* 3.9 23.1 - - + -
264I ILE* 3.9 21.1 - - + -
265I ALA* 5.2 0.7 - - - -
268I TYR* 4.0 32.8 - + + -
286I PHE* 3.5 48.9 - + + -
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Residues in contact with ARG 222 (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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112I LYS* 4.4 13.8 - - + +
166I ARG* 5.6 0.4 - - - +
180I TYR* 3.4 53.3 - - + +
183I LEU* 4.1 4.3 - - - -
215I SER* 3.9 5.9 + - - -
218I MET* 3.5 40.3 + - + +
219I GLU* 2.6 56.5 + - - +
221I PHE* 1.3 78.3 - - - +
223I PRO* 1.3 70.1 - - + +
225I VAL* 2.9 17.8 + - - +
226I ASP* 3.1 15.5 + - - +
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Residues in contact with PRO 223 (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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112I LYS* 4.3 3.6 - - + +
115I ASN* 3.7 38.8 - - + +
116I GLN* 4.0 14.4 - - + +
119I HIS* 4.8 1.6 - - + -
155I TYR* 4.3 5.6 - - - +
219I GLU 4.0 2.2 - - - +
220I PRO* 3.4 12.1 - - + +
221I PHE 3.4 4.3 - - - -
222I ARG* 1.3 94.8 - - + +
224I LEU* 1.3 52.0 - - - +
226I ASP* 3.4 17.8 - - + +
227I GLN* 2.8 39.3 + - - +
288I ILE* 4.2 14.6 - - + -
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Residues in contact with LEU 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I LEU* 5.4 1.6 - - + -
221I PHE* 2.9 21.3 + - + +
223I PRO* 1.3 78.2 - - - +
225I VAL* 1.3 62.9 + - + +
227I GLN* 3.7 16.0 - - - +
228I ILE* 3.3 25.3 + - - +
247I LEU* 3.9 13.9 - - + +
252I TYR* 3.5 36.8 - - + -
261I LEU* 4.0 28.5 - - + -
286I PHE* 3.8 22.7 - - + -
288I ILE* 3.6 26.7 - - + -
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Residues in contact with VAL 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I LEU* 3.9 18.4 - - + +
179I GLY* 3.7 37.5 - - - +
180I TYR* 4.0 9.9 - - + +
183I LEU* 3.7 28.0 - - + -
222I ARG 2.9 8.1 + - - +
224I LEU* 1.3 74.2 - - - +
226I ASP* 1.3 68.6 + - - +
228I ILE* 3.1 4.3 + - - +
229I ILE* 3.0 28.9 + - + +
244I LEU* 4.0 14.1 - - + -
247I LEU* 4.1 15.7 - - + -
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Residues in contact with ASP 226 (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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116I GLN* 4.9 3.3 + - - -
119I HIS* 3.8 5.2 - - + -
155I TYR* 2.8 41.2 + - + +
156I PHE* 4.3 4.3 - - + -
159I LEU* 5.1 2.6 - - + +
160I PHE* 5.1 3.0 - - + -
176I LEU* 3.2 18.8 - - + +
180I TYR* 2.5 28.4 + - - -
222I ARG* 3.1 10.8 + - - +
223I PRO* 3.1 18.5 + - - +
225I VAL* 1.3 76.5 - - - +
227I GLN* 1.3 56.8 + - - +
229I ILE* 3.3 1.0 + - - +
230I TYR* 2.8 32.9 + - - +
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Residues in contact with GLN 227 (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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119I HIS* 3.5 27.8 - - + -
122I GLN* 3.3 23.3 + - - +
123I ARG* 3.5 7.4 + - - +
223I PRO 2.8 20.5 + - - +
224I LEU* 3.7 27.2 - - - +
226I ASP* 1.3 74.4 - - - +
228I ILE* 1.3 68.1 + - + +
230I TYR* 3.3 0.5 + - - +
231I GLU* 3.0 34.9 + - - +
252I TYR* 5.4 2.1 - - - -
288I ILE* 3.7 29.7 + - + +
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Residues in contact with ILE 228 (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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224I LEU 3.3 17.0 - - - +
225I VAL* 3.1 7.2 + - - +
227I GLN* 1.3 84.0 - - + +
229I ILE* 1.3 64.1 + - + +
231I GLU* 3.3 17.6 + - - +
232I ASN* 2.9 32.4 + - - +
240I MET* 4.9 0.9 - - - +
243I LYS* 3.9 38.1 - - + +
244I LEU* 3.9 23.6 - - + +
246I ALA* 4.9 11.2 - - + -
247I LEU* 5.0 10.8 - - + -
250I ASN* 5.6 4.3 - - - +
252I TYR* 5.8 2.7 - - - +
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Residues in contact with ILE 229 (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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160I PHE* 4.5 6.1 - - + -
172I ILE* 3.9 36.8 - - + +
175I GLY* 3.4 39.3 - - - +
176I LEU* 3.9 11.9 - - + +
225I VAL* 3.0 18.1 + - + +
226I ASP 4.0 2.0 - - - +
228I ILE* 1.3 76.4 - - + +
230I TYR* 1.3 67.3 + - - +
232I ASN* 3.1 7.2 + - - +
233I ARG* 2.9 20.6 + - - -
240I MET* 4.4 17.5 - - + -
244I LEU* 3.6 31.0 - - + -
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Residues in contact with TYR 230 (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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119I HIS* 4.3 7.6 - - + -
123I ARG* 3.2 50.6 - - + +
125I TYR* 4.3 17.3 + - - -
159I LEU* 3.4 37.1 + - + -
160I PHE* 3.9 24.4 - + + -
226I ASP 2.8 22.0 + - - +
227I GLN 3.5 4.3 - - - +
229I ILE* 1.3 73.7 - - - +
231I GLU* 1.3 64.6 + - + +
232I ASN 3.1 1.0 + - - -
233I ARG* 3.0 69.9 + - - -
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Residues in contact with GLU 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I GLN* 4.3 5.7 + - - -
123I ARG* 3.1 34.3 + - - +
227I GLN* 3.0 25.6 + - - +
228I ILE* 3.7 19.6 - - - +
230I TYR* 1.3 78.0 - - + +
232I ASN* 1.3 66.3 + - - +
233I ARG* 3.5 2.8 + - - +
234I LYS* 6.1 0.5 - - - +
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Residues in contact with ASN 232 (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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228I ILE* 2.9 26.1 + - - +
229I ILE* 3.1 7.5 + - - +
231I GLU* 1.3 88.7 + - - +
233I ARG* 1.3 61.0 + - - +
234I LYS* 3.2 3.8 - - - -
235I GLU* 3.1 39.7 + - + +
239I ILE* 4.4 0.2 - - - +
240I MET* 3.7 24.3 - - + +
243I LYS* 3.8 45.7 - - - +
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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
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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