Contacts of the helix formed by residues 324 - 334 (chain B) in PDB entry 5UNG
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B GLN* 4.7 8.3 + - - +
257B MET* 4.0 14.2 - - + +
321B VAL* 3.4 42.2 + - - +
323B ASN* 1.3 76.1 - - + +
325B PHE* 1.4 56.6 + - - +
326B GLN 3.5 1.1 - - - -
327B GLN* 3.5 12.5 + - + +
328B LYS* 3.0 63.4 + - + +
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Residues in contact with PHE 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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142B ARG* 3.7 57.4 - - + +
145B SER* 6.4 0.2 - - - -
234B ILE* 5.1 6.7 - - + -
254B VAL* 3.6 33.9 - - + +
257B MET* 3.7 42.0 - - + +
258B ALA* 4.3 12.1 - - + -
322B GLY 3.8 13.7 - - - +
323B ASN 3.3 0.8 - - - -
324B ARG* 1.4 76.5 - - - +
326B GLN* 1.3 59.1 + - + +
328B LYS* 3.5 3.4 + - - +
329B LEU* 3.0 56.3 + - + +
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Residues in contact with GLN 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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79B SER* 6.0 2.5 - - - +
322B GLY 5.1 0.6 + - - -
323B ASN 4.2 8.5 + - - +
324B ARG 3.5 0.2 - - - -
325B PHE* 1.3 81.3 - - + +
327B GLN* 1.4 58.4 + - - +
329B LEU* 3.5 8.1 + - - +
330B ARG* 3.2 27.2 + - - +
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Residues in contact with GLN 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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323B ASN 4.6 3.5 + - - +
324B ARG* 3.5 17.6 + - + +
325B PHE 3.3 0.6 - - - -
326B GLN* 1.4 78.2 - - - +
328B LYS* 1.3 53.6 + - + +
330B ARG* 3.5 10.7 + - - +
331B SER* 2.8 35.6 + - - -
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Residues in contact with LYS 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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250B THR* 4.4 18.0 - - + +
253B GLN* 3.5 47.0 + - + +
254B VAL* 3.8 19.1 - - + +
257B MET* 5.3 4.2 - - - -
324B ARG* 3.0 63.1 + - + +
325B PHE* 4.1 1.8 - - - +
327B GLN* 1.3 74.0 - - + +
329B LEU* 1.4 59.1 + - - +
330B ARG 3.3 0.2 - - - -
331B SER* 3.5 10.2 - - - +
332B VAL* 3.3 31.5 + - - +
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Residues in contact with LEU 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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142B ARG 5.0 0.4 - - - +
145B SER* 3.8 38.6 - - - +
146B VAL* 3.8 24.9 - - + -
238B LEU* 5.7 2.5 - - + -
254B VAL* 3.9 22.4 - - + +
325B PHE* 3.0 41.5 + - + +
326B GLN* 3.7 10.1 - - - +
327B GLN 3.3 0.4 - - - -
328B LYS* 1.4 75.5 - - - +
330B ARG* 1.3 59.1 + - - +
332B VAL* 3.3 22.0 - - + +
333B PHE* 3.5 13.0 + - - +
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Residues in contact with ARG 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 GLN 3.2 16.7 + - - +
327B GLN* 3.7 14.4 - - - +
328B LYS 3.3 0.2 - - - -
329B LEU* 1.3 75.3 - - - +
331B SER* 1.4 58.8 + - - +
333B PHE* 3.9 5.2 - - - +
334B ARG* 2.9 30.4 + - - +
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Residues in contact with SER 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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247B ASN* 4.6 8.0 - - - +
250B THR* 4.8 16.4 - - - -
327B GLN* 2.8 21.7 + - - -
328B LYS* 3.5 14.2 - - - +
329B LEU 3.3 0.6 - - - -
330B ARG* 1.4 75.6 - - - +
332B VAL* 1.4 62.9 + - - +
334B ARG* 3.5 14.7 + - - +
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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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238B LEU* 5.5 14.4 - - + -
247B ASN* 3.9 18.5 - - + +
250B THR* 3.4 25.8 - - - +
251B ARG* 3.9 22.9 - - + +
254B VAL* 5.3 4.3 - - + -
328B LYS 3.3 11.8 + - - +
329B LEU* 3.3 24.5 - - + +
331B SER* 1.4 76.1 - - - +
333B PHE* 1.3 58.6 + - + +
334B ARG* 5.1 1.1 - - - +
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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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149B PRO* 5.3 15.3 - - + -
329B LEU 3.5 14.9 + - - +
330B ARG* 4.2 5.4 - - - +
331B SER 3.3 0.4 - - - -
332B VAL* 1.3 79.8 - - + +
334B ARG* 1.4 68.2 + - - +
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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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330B ARG 2.9 19.8 + - - +
331B SER* 3.5 11.2 + - - +
332B VAL 3.5 1.9 - - - +
333B PHE* 1.4 82.2 - - - +
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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