Contacts of the helix formed by residues 314 - 325 (chain B) in PDB entry 5NER
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 GLN 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B THR* 5.9 0.7 - - - +
251B ASP 3.0 18.9 - - - +
252B ALA* 3.4 32.3 - - - +
253B ASP* 2.6 31.6 + - - +
310B VAL* 4.0 8.7 - - + -
311B THR* 3.2 17.0 - - - +
312B GLN 2.9 3.7 - - - +
313B GLU* 1.3 98.9 + - - +
315B VAL* 1.3 63.8 + - - +
316B HIS* 3.3 3.9 - - - +
317B LEU* 3.3 10.2 + - + +
318B TYR* 3.2 35.9 + - + -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.8 16.2 - - + +
311B THR 3.2 24.8 + - - +
312B GLN* 3.7 5.4 - - + -
313B GLU 4.3 0.2 - - - +
314B GLN* 1.3 78.2 - - - +
316B HIS* 1.3 67.3 + - + +
318B TYR* 3.5 0.9 + - - +
319B GLU* 3.0 45.0 + - - +
330B VAL* 4.4 12.5 - - + +
331B GLY 5.6 0.2 - - - -
332B LEU* 3.6 29.6 - - + +
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Residues in contact with HIS 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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248A ARG* 5.4 9.0 - - - +
313B GLU* 5.0 10.5 + - - -
314B GLN 5.0 6.3 - - - +
315B VAL* 1.3 85.0 - - + +
317B LEU* 1.3 59.5 + - - +
319B GLU* 3.1 22.4 + - - +
320B ASN* 2.7 30.2 + - - +
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Residues in contact with LEU 317 (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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248A ARG* 3.8 28.0 - - + +
249A THR* 3.7 27.6 - - + +
272A MET* 4.2 6.3 - - - -
253B ASP* 4.2 22.7 - - + +
254B SER 5.2 1.1 - - - +
314B GLN* 3.3 15.2 + - - +
316B HIS* 1.3 79.5 - - - +
318B TYR* 1.3 86.6 + - + +
320B ASN* 3.4 8.2 + - - +
321B TYR* 3.2 46.3 + - + +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 4.6 2.5 - + - -
248B PHE* 4.1 13.9 - + - -
250B SER* 4.9 0.2 + - - -
252B ALA 2.7 29.4 + - - -
253B ASP 3.2 4.7 + - - -
254B SER* 2.5 29.6 + - - -
308B PHE* 3.6 49.1 - + + -
310B VAL* 3.6 21.8 - - + -
314B GLN* 3.2 32.4 + - + +
315B VAL 4.4 0.2 - - - +
317B LEU* 1.3 91.7 - - + +
319B GLU* 1.3 58.7 + - - +
321B TYR* 3.8 20.9 - + - -
322B ALA* 3.0 29.1 + - - +
330B VAL* 3.4 8.1 - - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.0 31.6 + - - +
316B HIS* 3.1 17.7 + - - +
318B TYR* 1.3 78.3 - - - +
320B ASN* 1.3 62.9 + - - +
322B ALA* 3.3 4.7 + - + +
323B LYS* 3.2 34.5 + - - +
330B VAL* 3.5 31.3 - - + +
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Residues in contact with ASN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 4.3 18.7 + - - +
272A MET* 3.8 32.0 - - + +
316B HIS* 2.7 30.9 + - - +
317B LEU* 3.7 7.7 + - - +
318B TYR 3.3 0.2 - - - -
319B GLU* 1.3 76.1 - - - +
321B TYR* 1.3 65.5 + - - +
323B LYS* 3.4 41.7 + - + +
324B LEU* 3.8 11.8 - - - +
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Residues in contact with TYR 321 (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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249A THR* 3.1 37.6 + - - +
272A MET* 3.9 15.9 - - + -
273A ALA* 3.8 20.4 - - + -
223B PHE* 3.9 25.6 - + + -
254B SER* 4.6 5.2 + - - -
256B PHE* 3.9 14.4 - - - -
292B ILE* 4.2 15.3 - - + +
308B PHE* 4.3 10.8 - + + -
317B LEU* 3.2 39.4 + - + +
318B TYR* 3.7 24.0 - + - +
319B GLU 3.3 0.2 - - - -
320B ASN* 1.3 77.2 - - - +
322B ALA* 1.3 58.2 + - - +
324B LEU* 3.0 26.1 + - + +
325B ILE* 3.3 19.9 + - + +
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Residues in contact with ALA 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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308B PHE* 4.2 5.6 - - + -
318B TYR 3.0 18.6 + - - +
319B GLU* 3.7 5.4 - - - +
320B ASN 3.3 0.2 - - - -
321B TYR* 1.3 74.1 - - - +
323B LYS* 1.3 61.3 + - - +
324B LEU 3.2 0.4 - - - -
325B ILE* 2.9 24.7 - - - +
328B ALA* 3.7 40.0 - - + +
329B THR* 4.6 0.9 - - - -
330B VAL* 4.2 13.5 - - + -
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Residues in contact with LYS 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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303A ARG* 5.7 2.4 + - - -
319B GLU* 3.2 24.8 + - - +
320B ASN* 3.4 32.5 + - - +
321B TYR 3.2 0.8 - - - -
322B ALA* 1.3 77.1 - - - +
324B LEU* 1.3 64.9 + - + +
325B ILE 4.8 1.4 - - - -
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Residues in contact with LEU 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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271A GLN* 4.6 21.5 - - + +
272A MET* 4.1 34.3 - - + +
301A MET* 5.3 3.6 - - - -
303A ARG* 6.0 2.5 - - - +
309A LEU* 3.9 26.4 - - + +
292B ILE* 4.3 15.7 - - + -
296B ILE* 3.3 23.9 - - + +
320B ASN 3.8 13.0 - - - +
321B TYR* 3.0 11.4 + - + +
323B LYS* 1.3 82.6 - - + +
325B ILE* 1.3 59.7 - - - +
326B PRO* 3.4 8.9 - - - +
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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
----------------------------------------------------------
223B PHE* 6.4 0.7 - - + -
292B ILE* 4.5 16.6 - - + -
295B LEU* 5.3 8.1 - - + -
296B ILE* 3.8 19.3 - - + -
299B LEU* 3.6 30.7 - - + -
304B VAL 6.1 0.2 - - - +
306B LEU* 4.2 20.9 - - + -
308B PHE* 4.4 13.2 - - + -
321B TYR* 3.3 20.7 + - + +
322B ALA 2.9 18.3 + - - +
323B LYS 4.8 1.3 - - - -
324B LEU* 1.3 78.9 - - - +
326B PRO* 1.3 74.5 - - + +
327B GLY 3.3 0.3 + - - -
328B ALA* 3.1 24.3 + - + -
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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