Contacts of the helix formed by residues 223 - 233 (chain I) in PDB entry 6QXT
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 ARG 223 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I MET 3.5 6.9 + - - +
220I GLU* 3.1 21.6 + - - +
221I PRO 3.4 0.6 - - - -
222I PHE* 1.3 77.9 - - - +
224I PRO* 1.3 63.8 - - - +
226I ILE* 3.0 22.8 + - - +
227I ASP* 3.6 3.9 + - - +
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Residues in contact with PRO 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I LYS 5.4 1.6 - - - +
116I ASN* 4.5 31.6 - - + +
117I GLN* 4.6 9.2 - - + +
120I TYR* 5.0 9.2 - - + +
220I GLU 4.8 0.2 - - - -
221I PRO 4.8 1.2 - - - +
222I PHE 3.4 1.0 - - - -
223I ARG* 1.3 77.9 - - - +
225I ILE* 1.3 61.8 + - - +
227I ASP* 3.0 13.6 + - + +
228I ARG* 2.9 23.2 + - - +
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Residues in contact with ILE 225 (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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222I PHE* 3.5 15.8 + - + +
223I ARG 3.1 1.2 + - - -
224I PRO* 1.3 78.0 - - - +
226I ILE* 1.3 60.8 + - - +
228I ARG* 3.7 12.0 + - - +
229I ILE* 3.8 11.4 + - - +
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Residues in contact with ILE 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I LEU* 5.8 4.7 - - - +
180I GLY* 4.7 22.9 - - - -
181I TYR 5.4 0.4 - - - +
222I PHE 4.3 1.5 + - - +
223I ARG* 3.0 13.1 + - - +
225I ILE* 1.3 76.9 - - - +
227I ASP* 1.3 60.3 + - - +
228I ARG 3.1 0.7 + - - -
229I ILE* 3.3 6.4 + - - +
230I VAL* 2.9 29.6 + - - +
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Residues in contact with ASP 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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160I LEU* 5.4 7.1 - - + +
223I ARG 3.6 2.5 + - - +
224I PRO* 3.0 17.8 + - + +
226I ILE* 1.3 79.0 - - - +
228I ARG* 1.3 57.8 + - - +
230I VAL* 3.8 8.8 - - - +
231I TYR* 2.9 29.1 + - - +
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Residues in contact with ARG 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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120I TYR* 6.1 4.9 - - + -
224I PRO 2.9 10.7 + - - +
225I ILE* 3.8 12.1 - - - +
226I ILE 3.1 0.2 - - - -
227I ASP* 1.3 75.0 - - - +
229I ILE* 1.3 60.2 + - - +
231I TYR* 3.0 7.9 + - - +
232I GLN* 2.9 27.5 + - - +
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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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225I ILE 3.8 7.6 + - - +
226I ILE* 3.3 7.7 + - - +
228I ARG* 1.3 79.3 - - - +
230I VAL* 1.3 57.5 + - - +
232I GLN* 3.8 7.1 - - - +
233I ASN* 2.9 34.5 + - - +
244I GLU* 5.4 16.6 - - + +
245I LEU* 5.8 3.6 - - + +
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Residues in contact with VAL 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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173I ILE* 5.4 8.5 - - + +
176I ALA* 5.0 17.3 - - + -
177I LEU* 5.5 6.5 - - + +
226I ILE 2.9 17.6 + - - +
227I ASP* 3.9 9.4 - - - +
229I ILE* 1.3 77.9 - - - +
231I TYR* 1.3 57.5 + - - +
233I ASN* 3.9 2.0 - - - -
234I ARG* 3.0 30.6 + - - +
241I ILE* 6.3 2.9 - - - -
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Residues in contact with TYR 231 (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 LEU* 4.7 24.0 - - + +
227I ASP 2.9 19.7 + - - +
228I ARG* 3.0 7.4 + - - +
230I VAL* 1.3 77.7 - - - +
232I GLN* 1.3 64.4 + - - +
234I ARG* 3.7 13.1 + - - +
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Residues in contact with GLN 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 ARG 2.9 14.5 + - - +
229I ILE* 3.3 7.2 + - - +
231I TYR* 1.3 80.5 - - - +
233I ASN* 1.3 58.2 + - + +
234I ARG 3.3 1.1 + - - -
235I HIS* 4.9 2.6 + - - +
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Residues in contact with ASN 233 (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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229I ILE 2.9 16.9 + - - +
230I VAL* 3.9 2.7 - - - +
232I GLN* 1.3 75.8 - - + +
234I ARG* 1.3 54.0 + - - +
235I HIS* 3.1 3.4 - - - -
236I ASN* 2.8 40.8 + - + +
240I LYS 5.5 0.4 - - - +
241I ILE* 4.9 14.7 - - + +
244I GLU* 4.7 19.1 - - + -
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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