Contacts of the helix formed by residues 324 - 334 (chain B) in PDB entry 2G5W
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 ASN 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B GLY 3.6 2.7 + - - +
323B PHE* 1.3 72.8 - - - +
325B LYS* 1.3 59.5 + - - +
326B GLU* 2.9 13.1 + - - +
327B LEU* 2.9 43.6 + - - +
328B GLY 3.1 8.3 + - - -
342B TYR* 2.6 31.5 + - - -
345B LEU* 4.3 13.2 - - + -
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Residues in contact with LYS 325 (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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12B LEU* 3.6 4.2 - - + +
13B PHE* 5.0 4.7 - - - -
324B ASN* 1.3 78.1 - - - +
326B GLU* 1.3 54.1 + - + +
328B GLY 3.2 2.1 + - - -
329B MET* 2.8 57.5 + - + +
342B TYR* 4.2 2.5 - - - -
356B PHE* 3.3 70.8 + - + +
357B LYS 5.5 0.6 + - - -
359B ASP* 3.6 33.6 + - - +
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Residues in contact with GLU 326 (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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324B ASN* 2.9 12.1 + - - +
325B LYS* 1.3 77.8 - - + +
327B LEU* 1.3 72.7 + - - +
329B MET* 3.3 9.4 + - + +
330B GLN* 2.8 37.7 + - + +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 4.3 23.1 - - - +
322B GLY 3.9 19.1 - - - +
323B PHE* 3.8 18.4 - - + -
324B ASN* 2.9 33.9 + - - +
326B GLU* 1.3 86.5 - - - +
328B GLY* 1.3 57.8 + - - +
330B GLN* 3.4 24.7 + - - +
331B ALA* 2.8 29.8 + - - +
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Residues in contact with GLY 328 (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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12B LEU* 3.6 11.1 - - - +
323B PHE* 3.7 10.0 - - - -
324B ASN 3.1 11.1 + - - -
327B LEU* 1.3 72.5 - - - +
329B MET* 1.3 65.3 + - - +
331B ALA* 3.8 0.9 - - - +
332B VAL* 3.3 30.8 + - - +
340B VAL* 4.1 6.3 - - - -
342B TYR* 3.4 20.9 - - - -
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Residues in contact with MET 329 (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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11B THR* 3.9 22.8 - - + -
12B LEU* 3.7 34.7 - - + +
13B PHE* 4.0 22.4 - - + -
325B LYS* 2.8 41.2 + - + +
326B GLU* 3.4 11.7 - - + +
328B GLY* 1.3 74.5 - - - +
330B GLN* 1.3 61.9 + - - +
332B VAL* 4.0 1.2 - - - +
333B GLN* 3.0 44.1 + - - +
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Residues in contact with GLN 330 (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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326B GLU* 2.8 25.8 + - + +
327B LEU* 3.5 28.9 + - - +
328B GLY 3.3 0.2 - - - -
329B MET* 1.3 73.0 - - - +
331B ALA* 1.3 62.8 + - - +
333B GLN* 3.4 6.1 + - - +
334B GLN* 3.0 59.1 + - - +
336B ASP* 5.8 0.2 + - - -
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Residues in contact with ALA 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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319B SER* 5.5 0.2 - - - +
323B PHE* 4.0 19.7 - - + -
327B LEU 2.8 20.4 + - - +
328B GLY* 3.8 5.6 - - - +
329B MET 3.4 0.2 - - - -
330B GLN* 1.3 75.4 - - - +
332B VAL* 1.3 60.7 + - - +
334B GLN* 3.6 0.4 + - - +
335B GLY 3.2 2.8 + - - -
336B ASP* 2.7 52.9 + - + +
337B ALA* 3.5 15.2 + - + -
340B VAL* 4.5 2.7 - - + -
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Residues in contact with VAL 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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10B GLU* 3.9 13.6 - - + +
11B THR 3.4 28.9 - - - +
12B LEU* 4.2 9.0 - - + -
26B ARG* 3.8 32.1 - - + +
328B GLY 3.3 16.4 + - - +
329B MET 4.1 0.9 - - - +
331B ALA* 1.3 74.0 - - - +
333B GLN* 1.3 66.2 + - - +
335B GLY* 3.1 12.5 + - - -
337B ALA 3.5 19.1 - - - +
338B ASP 4.3 2.0 - - - +
340B VAL* 3.9 19.3 - - + -
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Residues in contact with GLN 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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9B ASN* 4.0 20.4 + - - +
10B GLU 3.2 22.2 + - - +
11B THR* 3.9 19.7 - - + +
329B MET* 3.0 44.4 + - - +
330B GLN* 3.8 6.0 - - - +
332B VAL* 1.3 77.4 - - - +
334B GLN* 1.3 61.8 + - + +
335B GLY 3.2 0.6 + - - -
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Residues in contact with GLN 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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307B LYS* 3.5 12.3 + - - -
330B GLN* 3.0 49.1 + - - +
333B GLN* 1.3 76.9 - - + +
335B GLY* 1.3 61.0 + - - +
336B ASP* 2.8 30.8 + - - +
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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