Contacts of the helix formed by residues 315 - 328 (chain B) in PDB entry 4BL8
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 ASP 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B LEU* 2.9 17.5 + - + +
313B ALA 3.7 2.6 - - - +
314B LYS* 1.3 76.4 - - - +
316B PRO* 1.3 74.4 - - - +
317B ARG* 2.9 56.6 + - - +
318B ILE* 2.9 27.2 + - + +
319B ALA 3.2 7.3 + - - -
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Residues in contact with PRO 316 (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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54A THR* 5.1 23.3 - - + -
245B VAL 4.6 3.5 - - - +
314B LYS 3.0 10.3 - - - +
315B ASP* 1.3 91.1 - - - +
317B ARG* 1.3 65.7 + - + +
319B ALA* 3.1 13.1 + - + +
320B ALA* 3.0 24.4 + - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TRP* 3.2 63.0 - - + +
237B ASP* 3.8 13.9 + - - -
243B TYR* 2.9 36.1 + - + -
244B GLY* 6.2 0.4 - - - -
245B VAL* 4.0 22.9 - - + +
295B ASN* 6.0 1.6 - - - +
299B PRO* 4.4 10.9 - - - +
315B ASP* 2.9 30.9 + - - +
316B PRO* 1.3 82.8 - - + +
318B ILE* 1.3 59.2 + - - +
320B ALA* 3.5 2.9 + - - +
321B THR* 3.2 16.8 + - - -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TRP* 3.8 21.5 - - + -
295B ASN* 5.8 1.6 - - - +
299B PRO* 5.9 1.1 - - + -
301B GLY* 3.0 28.9 - - - +
302B ALA* 3.7 28.3 - - + +
309B GLU* 4.5 9.9 - - - +
312B LEU* 4.0 20.2 - - + +
313B ALA* 4.8 5.4 - - - +
315B ASP* 2.9 31.2 + - + +
317B ARG* 1.3 74.1 - - - +
319B ALA* 1.3 66.5 + - - +
321B THR* 3.1 14.0 + - - -
322B MET* 3.1 17.4 + - + +
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Residues in contact with ALA 319 (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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313B ALA 4.9 7.2 + - - +
314B LYS 5.6 0.4 - - - +
315B ASP 3.2 3.8 + - - +
316B PRO* 3.1 19.2 + - + +
318B ILE* 1.3 81.6 - - - +
320B ALA* 1.3 55.7 + - - +
322B MET* 3.5 6.0 + - - +
323B GLU* 3.1 27.5 + - - +
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Residues in contact with ALA 320 (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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115B SER* 3.8 2.0 - - - -
245B VAL* 3.2 37.7 - - + +
246B THR* 3.7 12.7 - - - +
316B PRO 3.0 13.0 + - - +
317B ARG 3.9 4.7 - - - +
319B ALA* 1.3 74.3 - - - +
321B THR* 1.3 66.1 + - - +
323B GLU* 3.7 11.4 - - - +
324B ASN* 3.2 28.6 + - - -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL 4.2 14.1 - - - +
112B GLU 4.6 0.2 - - - -
113B ALA* 3.6 32.7 + - + +
115B SER* 3.5 13.2 + - - -
230B PRO* 3.8 12.5 - - + +
233B TRP* 3.5 19.3 - - - -
301B GLY* 5.6 0.4 - - - -
302B ALA 5.1 3.6 - - - +
317B ARG 3.2 13.5 + - - -
318B ILE* 3.1 13.8 + - - +
320B ALA* 1.3 76.7 - - - +
322B MET* 1.3 66.9 + - - +
324B ASN* 3.3 4.0 + - - +
325B ALA* 2.9 24.1 + - + +
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Residues in contact with MET 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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93B PHE* 4.8 16.8 - - + -
111B VAL* 4.2 23.8 - - + -
302B ALA* 3.4 32.3 - - + -
309B GLU* 6.1 0.2 - - - +
318B ILE* 3.1 17.9 + - + +
319B ALA* 4.0 6.1 - - - +
320B ALA 3.3 0.2 - - - -
321B THR* 1.3 77.0 - - + +
323B GLU* 1.3 59.5 - - - +
325B ALA* 3.6 12.3 - - + +
326B GLN* 3.0 38.2 + - - +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 4.1 27.8 + - + +
319B ALA 3.1 17.9 + - - +
320B ALA* 3.7 11.4 - - - +
321B THR 3.3 0.6 - - - -
322B MET* 1.3 77.9 - - - +
324B ASN* 1.3 62.4 + - - +
326B GLN* 3.4 14.2 + - - +
327B LYS* 3.4 36.8 + - - +
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Residues in contact with ASN 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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113B ALA* 4.8 0.7 - - + -
114B LEU 3.3 19.1 - - - +
115B SER* 3.1 28.3 + - - +
246B THR 3.1 20.6 + - - -
247B VAL* 3.3 16.1 - - - +
248B LEU* 3.0 28.0 + - - +
256B SER 5.1 2.4 - - - +
258B PRO* 3.3 18.6 - - + +
320B ALA 3.2 8.9 + - - -
321B THR 3.7 6.3 - - - +
323B GLU* 1.3 76.9 - - - +
325B ALA* 1.3 60.8 + - - +
327B LYS* 3.4 5.9 + - - +
328B GLY 3.0 22.5 + - - -
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Residues in contact with ALA 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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111B VAL* 4.8 4.7 - - + -
113B ALA* 3.7 10.7 - - + +
260B VAL* 3.3 40.4 - - + +
321B THR* 2.9 16.4 + - + +
322B MET* 3.6 23.3 - - + +
323B GLU 3.3 0.4 - - - -
324B ASN* 1.3 76.4 - - - +
326B GLN* 1.3 64.6 + - - +
328B GLY 3.5 8.0 + - - +
329B GLU* 5.2 0.2 - - - -
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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
----------------------------------------------------------
564A ARG* 5.2 7.7 - - - +
572A PRO* 4.3 31.2 + - + +
322B MET* 3.0 25.8 + - - +
323B GLU* 3.6 7.9 - - - +
324B ASN 3.2 0.2 - - - -
325B ALA* 1.3 79.0 - - - +
327B LYS* 1.3 64.3 + - + +
328B GLY 3.5 6.8 + - - +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 5.8 1.6 - - - -
421A SER* 4.8 9.8 + - - -
422A ALA* 5.0 15.3 - - + -
247B VAL* 3.8 28.9 - - + +
250B THR* 5.8 4.4 - - - +
255B PRO* 3.8 32.9 - - + +
256B SER 4.2 11.0 - - - +
257B LYS* 3.5 23.2 - - - +
323B GLU* 3.4 32.1 + - - +
324B ASN* 3.4 7.0 + - - +
325B ALA 3.3 0.2 - - - -
326B GLN* 1.3 75.0 - - + +
328B GLY* 1.3 65.0 + - - +
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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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257B LYS* 3.7 14.8 - - - -
258B PRO* 3.2 17.0 - - - +
324B ASN 3.0 14.2 + - - -
325B ALA 3.5 8.9 + - - +
326B GLN 3.3 9.5 - - - +
327B LYS* 1.3 82.9 - - - +
329B GLU* 1.3 68.6 + - - +
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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