Contacts of the helix formed by residues 321 - 332 (chain B) in PDB entry 4J15
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 PHE 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B ARG* 3.5 21.8 - - + -
198B LEU* 3.9 20.6 - - + -
201B GLY* 3.5 28.0 - - - -
204B HIS* 6.3 2.0 - + - -
205B LEU* 4.8 4.7 - - + -
316B GLY 4.0 5.6 - - - -
317B LEU* 2.8 31.2 + - + +
320B ARG* 1.3 103.5 - - + +
322B GLN* 1.3 59.1 + - - +
323B THR 3.4 2.5 - - - -
324B GLU* 3.4 35.5 - - + +
325B ILE* 2.9 28.6 + - - +
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Residues in contact with GLN 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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317B LEU 3.8 1.4 + - - -
318B GLN* 3.2 34.7 - - - +
319B GLU 5.1 4.5 - - - +
320B ARG 3.5 2.2 + - - +
321B PHE* 1.3 74.3 - - - +
323B THR* 1.3 64.8 + - + +
325B ILE* 3.1 17.1 + - - +
326B GLN* 2.8 55.2 + - + +
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Residues in contact with THR 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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49B ARG* 5.8 4.0 + - - +
84B GLN* 4.4 5.3 + - - -
85B PHE* 5.4 12.0 - - + -
322B GLN* 1.3 78.3 - - + +
324B GLU* 1.3 72.2 + - - +
326B GLN* 3.3 7.7 + - - +
327B THR* 2.9 32.7 + - - -
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Residues in contact with GLU 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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84B GLN* 3.6 24.6 - - - +
194B ALA* 3.4 40.0 - - + +
197B ARG* 4.3 10.2 - - - +
198B LEU* 4.5 6.3 - - + +
320B ARG 4.0 4.0 - - - +
321B PHE* 3.4 54.5 - - + +
323B THR* 1.3 92.0 + - - +
325B ILE* 1.3 59.2 + - - +
327B THR 3.3 0.3 + - - -
328B VAL* 3.3 21.7 + - - +
481B LEU* 5.0 0.2 - - - +
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Residues in contact with ILE 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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198B LEU* 3.6 18.2 - - + -
317B LEU 3.4 24.2 - - - +
318B GLN* 4.2 10.3 - - + -
321B PHE 2.9 25.4 + - - +
322B GLN* 3.1 22.0 + - - +
324B GLU* 1.3 71.8 - - - +
326B GLN* 1.3 63.1 + - - +
328B VAL* 3.3 4.5 + - - +
329B ASN* 2.9 27.5 + - + +
336B PRO* 6.4 2.5 - - + -
480B PHE* 3.8 28.0 - - + -
481B LEU* 4.4 13.8 - - + +
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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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322B GLN* 2.8 43.3 + - + +
323B THR* 3.5 7.2 - - - +
325B ILE* 1.3 74.6 - - - +
327B THR* 1.3 66.7 + - - +
329B ASN* 3.2 32.6 + - - +
330B LYS* 3.1 34.6 + - + +
336B PRO* 6.3 1.0 - - - +
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Residues in contact with THR 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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84B GLN* 3.8 12.8 + - + +
190B SER* 3.4 47.1 - - - +
191B THR* 4.1 7.8 + - - +
194B ALA* 3.8 8.7 - - + -
323B THR* 2.9 20.0 + - - -
324B GLU 3.6 6.5 - - - -
325B ILE 3.3 0.6 - - - -
326B GLN* 1.3 77.2 - - - +
328B VAL* 1.3 62.4 + - - +
330B LYS* 3.6 23.3 - - - +
331B GLN* 3.7 3.6 + - - +
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Residues in contact with VAL 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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191B THR* 4.2 11.0 - - + +
194B ALA* 3.9 12.1 - - + -
195B VAL* 3.7 26.7 - - + +
324B GLU 3.3 14.2 + - - +
325B ILE 3.9 5.2 - - - +
326B GLN 3.2 0.4 - - - -
327B THR* 1.3 75.0 - - - +
329B ASN* 1.3 52.9 + - - +
331B GLN* 3.1 3.5 + - - +
332B PHE* 2.6 41.5 + - + -
481B LEU* 4.1 31.4 - - + +
483B LEU* 4.0 29.2 - - + -
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Residues in contact with ASN 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 ILE* 2.9 20.4 + - + +
326B GLN* 3.2 36.0 + - - +
328B VAL* 1.3 75.3 - - - +
330B LYS* 1.3 63.7 + - - +
332B PHE 3.8 5.4 - - - -
333B PRO* 3.0 30.1 - - - +
334B CYS* 2.9 40.2 + - + +
336B PRO* 6.3 0.4 - - - +
481B LEU* 5.8 0.2 - - - +
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Residues in contact with LYS 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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162B PRO* 3.9 13.5 - - - +
190B SER* 5.9 1.2 + - - -
326B GLN* 3.1 22.8 + - + +
327B THR* 3.6 17.6 - - - +
328B VAL 3.3 0.2 - - - -
329B ASN* 1.3 76.8 - - - +
331B GLN* 1.3 60.9 + - - +
333B PRO* 4.4 5.9 - - - +
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Residues in contact with GLN 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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159B ALA 2.9 23.0 + - - +
160B VAL* 3.3 34.5 - - - +
161B ARG 4.0 12.5 + - - +
162B PRO* 4.2 19.4 - - + +
179B ARG* 4.5 5.5 - - - +
191B THR* 2.5 43.7 + - - +
327B THR 3.7 2.7 + - - +
328B VAL 3.1 5.0 + - - +
330B LYS* 1.3 79.4 - - - +
332B PHE* 1.3 98.3 + - + +
333B PRO* 3.6 6.3 - - - +
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Residues in contact with PHE 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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162B PRO* 6.2 0.9 - - + -
179B ARG* 6.0 3.6 - - - -
191B THR* 4.1 10.5 - - + -
328B VAL* 2.6 25.7 + - + +
329B ASN* 3.1 7.5 - - - +
331B GLN* 1.3 119.9 - - + +
333B PRO* 1.3 70.1 - - - +
334B CYS* 3.4 8.7 + - - +
481B LEU 4.2 3.6 - - - +
482B GLY 5.5 3.1 - - - +
483B LEU* 3.6 27.6 - - + -
484B HIS* 6.0 3.6 - - + -
488B GLN* 3.4 26.5 - - - -
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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