Contacts of the helix formed by residues 330 - 338 (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 PRO 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.7 39.0 - - + -
111B MET* 4.1 5.8 - - - -
328B ASN 4.7 0.9 - - - +
329B GLN* 1.3 100.1 - - + +
331B GLU* 1.3 64.7 + - - +
332B TRP* 3.3 27.1 - - + +
333B PHE* 3.2 27.8 + - + +
334B ARG* 3.4 6.4 + - - +
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Residues in contact with GLU 331 (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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204A ARG* 3.4 25.1 + - - +
227A GLU* 4.0 10.2 - - - +
230A ARG* 3.6 25.0 + - - +
329B GLN 3.5 3.0 + - - -
330B PRO* 1.3 73.3 - - - +
332B TRP* 1.3 59.4 + - - +
334B ARG* 3.3 9.6 + - - +
335B ASN* 2.9 47.5 + - - +
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Residues in contact with TRP 332 (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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30A ILE* 4.3 12.4 - - + +
202A GLU* 4.4 12.3 - - + +
203A GLU* 3.0 49.5 + - + +
204A ARG* 4.1 17.4 - - - +
205A PHE* 3.7 17.9 - - + +
111B MET* 4.1 33.0 - - + -
114B VAL* 4.1 23.1 - - + -
115B GLN* 4.4 15.7 - - + -
164B ILE* 6.3 0.9 - - + -
330B PRO* 3.5 24.1 - - + +
331B GLU* 1.3 79.2 - - - +
333B PHE* 1.3 81.8 + + - +
335B ASN* 3.2 10.7 + - - +
336B VAL* 2.9 44.2 + - + +
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Residues in contact with PHE 333 (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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107B CYS* 3.4 50.5 - - + -
110B THR* 3.8 20.0 - - + -
111B MET* 3.6 27.6 - - + -
114B VAL* 4.7 5.6 - - + -
258B LEU* 5.4 0.2 - - + -
326B THR* 4.5 5.4 - - + -
329B GLN* 4.2 17.7 - - + -
330B PRO* 3.2 21.5 + - + +
332B TRP* 1.3 98.7 - + + +
334B ARG* 1.3 57.4 + - - +
336B VAL* 3.2 5.0 + - + +
337B LEU* 2.9 58.1 + - + +
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Residues in contact with ARG 334 (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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230A ARG* 3.4 33.1 + - - +
234A ASP* 2.8 42.3 + - - +
322B ILE* 6.1 0.4 - - - -
323B THR* 3.1 40.4 + - - +
326B THR* 2.7 45.6 + - - +
328B ASN* 4.6 4.9 - - - +
329B GLN* 4.0 17.0 + - + +
330B PRO 3.5 10.5 - - - +
331B GLU* 3.3 8.2 + - - +
333B PHE* 1.3 76.1 - - - +
335B ASN* 1.3 55.7 + - - +
337B LEU* 4.9 0.9 - - - -
338B SER* 2.5 40.3 + - - -
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Residues in contact with ASN 335 (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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204A ARG* 5.2 4.6 - - - +
205A PHE* 3.4 32.4 + - + +
207A ILE* 3.7 23.5 - - + +
212A ARG* 5.3 4.6 + - - +
230A ARG* 3.2 25.6 + - - -
331B GLU* 2.9 40.6 + - - +
332B TRP* 3.2 6.3 + - - +
334B ARG* 1.3 77.3 - - - +
336B VAL* 1.3 57.2 + - - +
338B SER* 3.7 6.1 + - - -
339B ILE* 3.1 29.6 - - - +
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Residues in contact with VAL 336 (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* 3.4 36.8 - - + -
114B VAL* 5.1 7.4 - - + -
164B ILE* 3.9 14.6 - - + -
167B LEU* 4.9 5.4 - - + -
251B PHE* 4.0 9.0 - - + +
254B PHE* 4.0 29.2 - - + -
332B TRP* 2.9 30.0 + - + +
333B PHE* 3.7 7.0 - - + +
334B ARG 3.2 0.2 - - - -
335B ASN* 1.3 77.4 - - - +
337B LEU* 1.3 72.3 + - + +
338B SER 3.2 0.9 + - - -
339B ILE* 3.4 19.7 + - - +
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Residues in contact with LEU 337 (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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110B THR* 4.3 2.9 - - + -
114B VAL* 5.0 0.7 - - + -
251B PHE* 5.6 0.6 - - - +
254B PHE* 3.7 40.6 - - + +
255B VAL* 3.4 27.8 - - + +
258B LEU* 3.6 31.2 - - + -
322B ILE* 4.0 15.8 - - + +
326B THR* 3.9 13.9 - - + -
333B PHE* 2.9 54.8 + - + +
334B ARG 4.4 1.3 - - - +
336B VAL* 1.3 81.9 - - + +
338B SER* 1.3 57.7 + - - +
339B ILE 3.2 3.9 + - - -
340B ALA 4.1 0.9 + - - -
341B PRO* 3.7 5.2 - - - +
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Residues in contact with SER 338 (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* 5.0 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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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