Contacts of the helix formed by residues 321 - 332 (chain B) in PDB entry 1G4C
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 ARG 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 5.8 5.9 - - - +
80A GLN* 6.3 0.8 - - - +
315B HIS* 3.7 12.7 - - - -
316B TYR* 3.8 24.6 + - - -
317B ASP* 3.4 29.6 + - - +
318B MET 3.0 8.7 + - - +
319B LYS 3.3 1.4 + - - -
320B ASN* 1.3 86.3 - - - +
322B GLY* 1.3 65.3 + - - +
323B PHE* 3.4 40.6 - - + -
324B MET* 3.0 37.1 + - + +
325B LEU* 2.9 24.6 + - - +
352B PHE* 4.3 3.1 - - - -
363B MG 4.3 6.9 - - - -
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Residues in contact with GLY 322 (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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320B ASN 3.9 2.4 + - - -
321B ARG* 1.3 71.2 - - - +
323B PHE* 1.3 58.5 + - - +
325B LEU* 4.4 2.0 - - - -
326B TRP* 2.9 48.3 + - - +
352B PHE* 3.8 31.2 - - - -
355B LEU* 4.4 7.1 - - - +
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Residues in contact with PHE 323 (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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242B THR* 3.9 16.8 - - + -
255B ASN* 3.6 28.3 - - + +
256B ALA 5.2 1.2 + - - +
321B ARG* 3.1 40.6 - - + -
322B GLY* 1.3 76.5 - - - +
324B MET* 1.3 83.5 + - + +
327B PRO* 3.3 20.4 - - - +
355B LEU* 3.7 25.4 - - + +
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Residues in contact with MET 324 (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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206B ALA* 4.1 18.6 - - + -
257B ALA* 5.1 0.2 - - - +
297B ASP* 3.6 22.7 - - + +
299B MET* 3.8 29.1 - - - +
315B HIS* 3.7 19.1 - - - +
318B MET* 3.9 23.1 - - + +
321B ARG* 3.0 39.6 + - + +
323B PHE* 1.3 104.0 - - + +
325B LEU* 1.3 67.0 + - + +
326B TRP 3.5 0.4 - - - -
327B PRO* 3.6 2.0 - - - +
328B LEU* 3.2 23.2 + - - +
363B MG 4.3 1.8 - - - -
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Residues in contact with LEU 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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318B MET* 3.5 39.3 - - + +
319B LYS* 3.5 29.4 - - - +
321B ARG 2.9 18.0 + - - +
322B GLY* 4.3 1.6 - - - +
324B MET* 1.3 79.7 - - - +
326B TRP* 1.3 52.6 + - - +
328B LEU* 3.2 4.8 + - + +
329B PHE* 2.8 36.3 + - - +
337B PHE* 4.2 4.9 - - + -
343B LEU* 3.9 21.3 - - + +
346B ILE* 3.9 18.4 - - + -
347B LEU* 3.9 18.3 - - + +
352B PHE* 3.8 15.5 - - + -
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Residues in contact with TRP 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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240B TYR* 4.6 8.9 + - + -
322B GLY* 2.9 32.9 + - - +
325B LEU* 1.3 71.9 - - - +
327B PRO* 1.3 67.4 - - + +
329B PHE* 3.2 31.1 + + - +
330B GLU* 3.1 21.1 + - - +
347B LEU* 3.9 37.0 - - + +
351B ALA* 5.6 0.7 - - - -
352B PHE* 3.4 23.9 + - + +
353B ASP 3.1 26.5 + - - -
354B LYS* 3.8 44.6 - - + -
355B LEU* 4.4 14.6 - - + -
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Residues in contact with PRO 327 (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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237B SER* 3.6 28.1 - - - +
240B TYR* 3.5 35.0 - - + -
255B ASN 4.7 1.6 - - - +
256B ALA* 4.1 6.7 - - - -
257B ALA* 3.8 17.2 - - + +
322B GLY 3.7 1.6 - - - +
323B PHE* 3.3 28.5 - - - +
324B MET 3.6 5.2 - - - +
326B TRP* 1.3 95.4 - - + +
328B LEU* 1.3 61.9 + - - +
330B GLU* 3.2 12.0 + - + +
331B ILE* 3.5 7.8 + - - +
355B LEU* 5.4 0.7 - - + -
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Residues in contact with LEU 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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204B TYR* 3.4 45.5 - - + -
257B ALA* 3.9 4.8 - - + +
299B MET* 4.2 11.2 - - + -
300B LEU* 4.3 5.8 - - + -
318B MET* 4.0 26.9 - - + -
324B MET 3.2 16.3 + - - +
325B LEU* 3.2 4.8 + - + +
326B TRP 3.2 1.2 - - - -
327B PRO* 1.3 80.1 - - - +
329B PHE* 1.3 58.6 + - - +
331B ILE* 3.1 8.3 + - + +
332B ALA* 2.8 25.9 + - + +
335B LEU* 4.0 18.8 - - + -
337B PHE* 4.6 0.7 - - + -
343B LEU* 3.8 25.8 - - + -
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Residues in contact with PHE 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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325B LEU 2.8 12.5 + - - +
326B TRP* 3.7 29.6 - + - +
328B LEU* 1.3 73.6 - - - +
330B GLU* 1.3 65.4 + - - +
332B ALA 3.9 1.6 - - - -
333B PRO* 3.3 55.4 - - + +
343B LEU* 3.5 16.5 - - + +
344B ARG* 4.1 18.6 - - + -
347B LEU* 3.3 28.9 - - + -
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Residues in contact with GLU 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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237B SER* 3.4 8.5 - - - -
238B SER* 2.6 47.3 + - - -
240B TYR* 2.8 23.8 + - - +
326B TRP 3.1 12.7 + - - +
327B PRO 3.5 8.1 - - - +
328B LEU 3.1 0.4 - - - -
329B PHE* 1.3 83.5 - - - +
331B ILE* 1.3 61.8 + - + +
333B PRO* 4.3 4.5 - - - +
357B LYS* 4.6 2.3 + - - -
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Residues in contact with ILE 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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204B TYR* 4.0 22.6 + - + -
235B THR* 3.6 27.3 - - + +
236B VAL 3.8 2.5 - - - +
237B SER* 3.5 34.5 - - - +
257B ALA* 3.8 20.4 - - + +
258B VAL 3.9 3.4 - - - -
259B ALA* 3.7 30.5 - - + +
327B PRO 3.5 3.8 + - - +
328B LEU* 3.1 9.8 + - - +
330B GLU* 1.3 81.1 - - + +
332B ALA* 1.3 61.1 - - - +
333B PRO* 3.8 4.3 - - - +
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Residues in contact with ALA 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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204B TYR* 3.6 28.9 - - + +
328B LEU 2.8 12.3 + - - +
329B PHE 3.7 2.9 - - - -
331B ILE* 1.3 80.5 - - - +
333B PRO* 1.3 67.6 - - - +
334B GLU 3.1 4.1 + - - -
335B LEU* 3.1 34.8 + - + +
343B LEU* 3.6 7.4 - - - +
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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