Contacts of the helix formed by residues 338 - 346 (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 SER 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 5.0 2.6 - - - +
226A LEU* 5.7 3.9 - - - +
230A ARG* 5.0 6.4 + - - -
319B LEU* 3.7 23.9 - - - +
322B ILE* 4.7 8.7 - - - +
323B THR* 5.3 2.2 - - - -
334B ARG* 2.5 26.0 + - - -
335B ASN* 3.7 9.9 + - - -
337B LEU* 1.3 76.1 - - - +
339B ILE* 1.3 62.5 + - - +
340B ALA 3.5 0.4 - - - -
341B PRO* 3.4 12.8 - - - +
342B ILE* 3.2 28.9 - - - +
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Residues in contact with ILE 339 (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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205A PHE* 4.3 2.9 - - + -
207A ILE* 4.3 19.3 - - + -
211A MET* 3.6 27.1 - - + -
171B MET* 3.6 28.5 - - + -
251B PHE* 3.5 38.8 - - + -
335B ASN 3.1 25.6 - - - +
336B VAL 3.4 6.3 - - - +
337B LEU 3.2 1.8 - - - -
338B SER* 1.3 79.0 - - - +
340B ALA* 1.3 61.1 + - - +
342B ILE* 3.1 10.5 + - + +
343B MET* 2.9 37.0 + - - +
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Residues in contact with ALA 340 (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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248B ILE* 4.6 9.4 - - + -
251B PHE* 3.7 36.0 - - + +
252B VAL* 4.1 3.8 - - + +
255B VAL* 4.1 3.8 - - + -
337B LEU 4.1 0.4 + - - -
339B ILE* 1.3 78.0 - - - +
341B PRO* 1.3 63.0 - - + +
343B MET* 3.3 7.4 + - - +
344B PHE* 2.9 35.4 + - + -
412B PHE* 4.0 19.5 - - + -
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Residues in contact with PRO 341 (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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218A SER* 4.2 1.9 + - - -
255B VAL* 4.7 0.4 - - + -
315B PRO* 3.4 35.2 - - + +
318B PHE* 4.3 6.5 - - + -
319B LEU* 3.6 22.7 - - + +
322B ILE* 3.8 24.9 - - + -
337B LEU 3.7 6.3 - - - +
338B SER* 3.4 17.9 - - - +
340B ALA* 1.3 95.0 - - + +
342B ILE* 1.3 56.1 + - - +
344B PHE* 3.3 3.3 + - + -
345B SER* 2.9 26.7 + - - -
412B PHE* 4.9 5.8 - - + -
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Residues in contact with ILE 342 (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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207A ILE* 5.6 3.4 - - + -
211A MET* 4.6 11.2 - - + -
214A LEU* 3.5 32.7 - - + +
215A ALA* 3.5 32.3 - - + +
218A SER* 4.0 15.7 - - - +
226A LEU* 4.8 7.6 - - + -
319B LEU* 4.4 13.7 - - + -
338B SER* 3.2 28.9 + - - +
339B ILE* 3.1 18.0 + - + +
341B PRO* 1.3 75.9 - - - +
343B MET* 1.3 64.2 + - - +
345B SER* 3.2 11.3 + - - -
346B ASN* 3.3 14.6 + - - +
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Residues in contact with MET 343 (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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211A MET* 4.2 10.8 - - + -
214A LEU* 6.0 1.1 - - + -
170B VAL* 5.5 0.7 - - + -
171B MET* 5.9 0.2 - - - -
174B MET* 3.9 23.6 - - + -
221B ALA 4.1 5.6 - - - +
222B LEU* 3.5 30.6 - - + +
247B GLN* 4.4 8.5 - - + -
248B ILE* 3.6 36.6 - - + +
251B PHE* 3.9 19.5 - - + -
339B ILE* 2.9 41.3 + - + +
340B ALA 3.8 3.8 - - - +
342B ILE* 1.3 75.6 - - - +
344B PHE* 1.3 60.4 + - - +
346B ASN 2.9 23.7 - - - +
347B LYS* 3.5 6.2 - - - +
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Residues in contact with PHE 344 (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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224B LEU* 4.7 9.9 - - + -
248B ILE* 3.6 36.6 - - + -
252B VAL* 4.4 5.4 - - + -
315B PRO* 3.4 21.0 - - + +
340B ALA* 2.9 17.5 + - + +
341B PRO* 4.8 0.4 - - + -
342B ILE 3.2 0.2 - - - -
343B MET* 1.3 77.9 - - - +
345B SER* 1.3 63.1 + - - +
346B ASN 3.3 0.2 - - - -
347B LYS* 2.7 49.3 + - + +
406B GLY 5.2 0.9 - - - +
407B MET* 5.8 6.7 - - + -
411B MET* 3.5 39.0 - - + -
412B PHE* 3.4 44.4 - + - -
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Residues in contact with SER 345 (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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218A SER* 3.2 34.3 + - - -
65B GLN* 3.6 1.4 - - - +
315B PRO* 3.6 13.2 - - - -
316B ARG* 2.6 31.5 + - - -
341B PRO 2.9 11.8 + - - -
342B ILE 3.2 5.3 + - - -
344B PHE* 1.3 77.7 - - - +
346B ASN* 1.3 65.5 + - - +
404B SER* 3.2 31.0 + - - -
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Residues in contact with ASN 346 (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* 3.1 52.0 - - + +
217A GLN* 4.0 10.9 + - - +
58B ASN* 3.8 11.9 - - - +
61B THR* 5.2 0.7 - - + -
65B GLN* 2.5 41.0 + - - +
222B LEU* 3.3 22.5 - - + +
316B ARG* 5.2 0.2 - - - +
342B ILE 3.3 10.8 + - - +
343B MET 2.9 11.2 - - - +
345B SER* 1.3 86.1 + - - +
347B LYS* 1.3 57.5 + - - +
348B MET* 4.3 4.9 - - - -
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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