Contacts of the helix formed by residues 212 - 220 (chain J) 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 PHE 212 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185J LEU* 5.5 10.3 - - + +
189J ALA* 6.1 1.6 - - - -
210J ASN* 3.2 4.7 - - + +
211J GLN* 1.3 77.6 - - + +
213J ASN* 1.3 58.7 + - - +
214J LEU 3.4 1.6 - - - -
215J ALA* 3.5 11.3 + - + -
216J SER* 2.8 33.4 + - - -
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Residues in contact with ASN 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J GLN 4.5 3.6 - - - +
202J GLY* 4.3 17.7 - - - +
208J GLN* 5.3 7.6 - - + +
210J ASN* 3.4 28.4 + - + +
211J GLN 3.4 2.6 - - - -
212J PHE* 1.3 77.0 - - - +
214J LEU* 1.3 58.5 + - - +
216J SER* 3.2 7.8 + - - -
217J ASP* 2.9 28.3 + - - +
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Residues in contact with LEU 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J MET 4.5 2.9 - - - +
199J THR* 3.4 22.0 + - - +
201J ILE 3.3 24.0 + - - +
202J GLY* 4.5 4.5 - - - -
203J LEU* 5.3 0.9 - - - +
212J PHE 3.4 0.2 - - - -
213J ASN* 1.3 78.6 - - - +
215J ALA* 1.3 58.7 + - - +
217J ASP* 3.1 9.7 + - - +
218J ILE* 2.9 28.8 + - - +
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Residues in contact with ALA 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J LEU* 4.1 9.1 - - + +
188J PHE* 3.8 9.2 - - + +
189J ALA* 3.7 39.9 - - + +
192J VAL* 5.2 5.6 - - + -
199J THR* 4.7 3.6 + - - -
211J GLN 5.5 1.1 - - - +
212J PHE* 3.5 13.7 + - + +
213J ASN 3.4 0.2 - - - -
214J LEU* 1.3 78.4 - - - +
216J SER* 1.3 57.8 + - - +
218J ILE* 3.8 6.6 - - - +
219J MET* 2.9 30.1 + - - +
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Residues in contact with SER 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J LEU* 5.8 6.2 - - - +
212J PHE* 2.8 20.5 + - - -
213J ASN* 3.5 7.0 - - - -
215J ALA* 1.3 75.5 - - - +
217J ASP* 1.3 60.5 + - - +
219J MET* 3.1 6.2 + - - +
220J GLU* 2.9 30.0 + - - +
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Residues in contact with ASP 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J TRP* 5.8 6.7 - - + -
109J ILE* 4.3 17.7 - - + +
203J LEU* 5.1 18.2 - - + +
204J LYS* 5.9 4.9 - - + +
213J ASN 2.9 13.3 + - - +
214J LEU* 3.1 11.0 + - - +
216J SER* 1.3 76.8 - - - +
218J ILE* 1.3 60.3 + - - +
220J GLU* 3.7 15.1 + - - +
221J PRO 5.2 0.2 - - - -
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Residues in contact with ILE 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J PHE* 5.1 7.0 - - + +
214J LEU 2.9 16.4 + - - +
215J ALA* 3.9 7.9 - - - +
216J SER 3.2 0.2 - - - -
217J ASP* 1.3 77.5 - - - +
219J MET* 1.3 58.4 + - - +
220J GLU 3.3 2.2 + - - -
221J PRO* 4.5 7.1 - - - +
222J PHE* 5.5 0.5 + - - +
270J THR* 5.9 8.3 - - - -
273J VAL* 6.0 6.5 - - + -
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Residues in contact with MET 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J LEU* 4.5 19.0 - - + +
185J LEU* 5.1 3.4 - - + -
188J PHE* 4.2 14.4 - - + -
215J ALA 2.9 19.4 + - - +
216J SER* 3.1 7.1 + - - +
218J ILE* 1.3 75.2 - - - +
220J GLU* 1.3 64.5 + - - +
221J PRO 3.4 1.8 - - - -
222J PHE* 3.4 18.7 + - + +
223J ARG* 3.9 8.3 + - - +
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Residues in contact with GLU 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ILE* 5.2 6.5 - - + +
110J ILE* 5.7 2.5 - - - -
113J LYS* 3.7 19.3 - - + +
216J SER 2.9 12.7 + - - +
217J ASP* 3.8 12.8 - - - +
218J ILE 3.3 2.4 - - - -
219J MET* 1.3 78.6 - - - +
221J PRO* 1.3 62.4 - - - +
222J PHE 3.2 0.7 + - - -
223J ARG* 3.5 16.9 + - - +
224J PRO 5.2 0.2 - - - -
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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