Contacts of the helix formed by residues 214 - 222 (chain B) in PDB entry 6QNW
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 LYS 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A THR* 3.4 24.8 - - + +
60B GLU* 5.1 7.5 + - - +
174B MET* 3.7 17.9 - - - +
175B ASP 5.0 2.5 - - - +
176B LYS 3.6 16.4 - - - +
177B GLU* 3.0 28.1 + - + +
179B MET 5.9 0.2 - - - +
213B ASN* 1.3 74.7 - - - +
215B ARG* 1.3 62.3 + - - +
217B TYR* 3.3 7.9 + - + +
218B LEU* 2.9 53.4 + - + +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU 4.1 17.0 - - - +
61B THR* 4.0 20.9 + - - +
62B GLY* 4.7 9.2 + - - -
213B ASN* 3.4 15.0 - - - +
214B LYS* 1.3 81.3 - - - +
216B SER* 1.3 59.4 + - - +
218B LEU* 3.1 9.5 + - - +
219B ILE* 2.9 43.8 + - + +
397B ILE* 4.9 16.2 - - - +
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B VAL* 3.8 15.2 - - - +
213B ASN* 3.5 21.3 + - - +
214B LYS 3.5 0.2 - - - -
215B ARG* 1.3 79.2 - - - +
217B TYR* 1.3 58.2 + - - +
219B ILE* 3.3 12.8 + - - +
220B ARG* 2.9 42.3 + - - +
398B ASP* 3.3 19.5 + - - -
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TRP* 3.9 39.9 - + - -
150B PHE* 3.9 6.6 - - - -
173B SER* 2.5 48.0 + - - -
174B MET* 3.8 18.1 - - + +
176B LYS 6.0 0.7 - - - -
179B MET* 4.5 23.6 - - + -
212B VAL* 4.2 6.6 - - + +
213B ASN 3.1 20.5 + - - +
214B LYS* 3.5 7.6 - - + +
215B ARG 3.2 0.2 - - - -
216B SER* 1.3 74.7 - - - +
218B LEU* 1.3 71.7 + - + +
220B ARG* 3.2 6.8 + - + +
221B ALA* 2.9 33.2 + - + +
247B GLN* 3.8 22.4 + - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 4.5 13.9 - - - +
214A LEU* 4.9 5.4 - - + -
60B GLU* 3.5 44.2 - - + +
61B THR* 4.6 9.0 - - + -
174B MET* 4.2 25.1 - - + +
214B LYS* 2.9 44.2 + - + +
215B ARG* 3.5 9.6 - - - +
217B TYR* 1.3 87.8 - - + +
219B ILE* 1.3 63.1 + - - +
221B ALA* 3.3 4.6 + - - +
222B LEU* 3.1 38.8 + - + +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 4.9 12.3 - - - +
215B ARG* 2.9 34.6 + - + +
216B SER* 3.5 10.8 - - - +
217B TYR 3.2 0.2 - - - -
218B LEU* 1.3 77.0 - - - +
220B ARG* 1.3 62.4 + - + +
222B LEU* 3.4 8.0 + - - +
223B THR* 3.2 22.1 + - + +
348B MET* 4.1 13.8 - - + +
397B ILE* 3.6 24.7 - - + -
398B ASP* 3.7 31.6 - - + +
400B THR* 3.6 28.0 - - + +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR* 4.9 7.1 - - - +
131B TRP* 3.1 57.4 + - + +
132B THR 4.5 3.0 + - - -
134B ASN* 4.2 28.2 - - - +
181B ILE* 4.2 16.0 - - - +
212B VAL* 4.7 16.1 - - - +
216B SER* 2.9 34.3 + - - +
217B TYR* 3.7 7.4 - - + +
219B ILE* 1.3 78.8 - - + +
221B ALA* 1.3 60.4 + - - +
223B THR* 3.1 24.9 + - + +
247B GLN* 4.6 1.6 - - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TRP* 5.6 0.2 - - - -
174B MET* 3.9 25.1 - - + -
217B TYR* 2.9 23.8 + - + +
218B LEU* 3.9 5.6 - - - +
219B ILE 3.3 0.2 - - - -
220B ARG* 1.3 77.6 - - - +
222B LEU* 1.3 60.4 + - + +
223B THR 3.5 2.1 + - - +
245B GLY* 5.1 2.4 - - - -
247B GLN* 3.5 36.1 - - + +
248B ILE* 3.7 20.4 - - - +
343B MET* 4.1 2.1 - - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.9 27.4 - - + -
61B THR* 4.4 15.5 - - + -
174B MET* 5.1 4.3 - - + -
218B LEU* 3.1 28.0 + - + +
219B ILE* 3.4 3.1 - - - +
220B ARG 3.3 0.4 - - - -
221B ALA* 1.3 80.6 - - + +
223B THR* 1.3 51.8 + - - +
224B LEU* 4.6 1.6 - - - -
248B ILE* 4.7 6.1 - - + -
343B MET* 3.5 48.2 - - + +
346B ASN* 3.3 25.6 - - + +
347B LYS* 3.3 6.6 - - - +
348B MET* 2.5 38.2 + - + +
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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