Contacts of the helix formed by residues 314 - 327 (chain E) in PDB entry 5TJ4
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 314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310E GLU 4.6 0.6 + - - -
311E LEU* 2.9 17.0 + - + +
312E ALA 3.6 6.4 - - - +
313E LYS* 1.3 77.3 - - - +
315E PRO* 1.4 71.9 - - - +
316E ARG* 2.7 68.6 + - - +
317E ILE* 3.4 13.5 + - + +
318E ALA* 3.4 16.6 + - - +
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Residues in contact with PRO 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E VAL 4.8 1.9 - - - +
313E LYS 3.5 6.0 - - - +
314E ASP* 1.4 90.1 - - - +
316E ARG* 1.3 61.1 + - + +
318E ALA* 3.4 10.3 + - + +
319E ALA* 3.0 25.8 + - - +
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E TRP* 3.5 52.4 + - + +
236E ASP* 5.7 2.4 - - - +
242E TYR* 2.7 47.5 + - + -
244E VAL* 3.7 23.9 - - + +
298E PRO* 5.3 5.1 - - - +
314E ASP* 2.7 35.3 + - - +
315E PRO* 1.3 72.6 - - + +
317E ILE* 1.3 60.0 + - - +
319E ALA* 3.4 3.9 + - - +
320E THR* 3.0 29.6 + - - -
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E TRP* 4.0 21.3 - - + -
294E ASN* 5.9 1.1 - - - +
298E PRO* 6.0 1.1 - - + -
300E GLY* 3.5 30.1 - - - +
301E ALA* 3.9 25.6 - - + +
308E GLU* 4.2 11.2 - - - +
311E LEU* 3.5 34.3 - - + +
312E ALA* 4.5 5.2 - - - -
314E ASP* 3.4 19.6 + - + +
315E PRO 3.3 0.4 - - - -
316E ARG* 1.3 72.7 - - - +
318E ALA* 1.3 61.9 + - - +
320E THR* 3.1 7.7 + - - +
321E MET* 2.9 30.7 + - + +
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Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E ALA 4.9 6.8 + - - +
314E ASP 3.4 10.8 + - - +
315E PRO* 3.5 12.1 - - + +
316E ARG 3.3 0.2 - - - -
317E ILE* 1.3 79.9 - - - +
319E ALA* 1.3 56.5 + - - +
321E MET* 3.3 7.0 + - - +
322E GLU* 2.9 29.2 + - - +
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Residues in contact with ALA 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E SER* 4.4 0.2 - - - -
244E VAL* 3.4 39.3 - - + +
245E THR* 4.0 10.1 - - - +
246E VAL* 4.9 1.5 - - - +
315E PRO 3.0 12.0 + - - +
316E ARG 3.5 9.0 - - - +
317E ILE 3.2 0.2 - - - -
318E ALA* 1.3 73.9 - - - +
320E THR* 1.3 64.6 + - - +
322E GLU* 3.4 8.2 + - - +
323E ASN* 2.9 30.6 + - - -
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Residues in contact with THR 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E VAL 4.7 3.8 - - - +
112E ALA* 3.8 27.7 - - + +
114E SER* 3.3 18.7 + - - -
229E PRO* 4.2 11.3 - - + +
232E TRP* 3.6 17.3 - - - -
301E ALA 5.0 4.3 - - - +
316E ARG 3.0 14.6 + - - -
317E ILE* 3.1 12.1 + - - -
319E ALA* 1.3 76.6 - - - +
321E MET* 1.3 75.4 + - + +
323E ASN* 3.2 5.3 + - - +
324E ALA* 2.8 26.2 + - - +
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Residues in contact with MET 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E PHE* 5.9 4.9 - - - -
110E VAL* 3.8 28.5 - - + +
112E ALA* 5.6 0.2 - - + -
301E ALA* 3.5 33.4 - - + -
308E GLU* 5.1 3.8 - - - +
317E ILE* 2.9 22.2 + - + +
318E ALA* 3.3 6.9 + - - +
320E THR* 1.3 91.0 - - + +
322E GLU* 1.3 60.0 + - - +
324E ALA* 3.6 13.1 - - + +
325E GLN* 2.8 44.4 + - + +
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Residues in contact with GLU 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E VAL* 3.7 25.4 - - + -
318E ALA 2.9 15.8 + - - +
319E ALA* 3.7 7.6 - - - +
321E MET* 1.3 76.4 - - - +
323E ASN* 1.3 57.2 + - - +
325E GLN* 3.5 10.9 + - + +
326E LYS* 3.1 45.4 + - + +
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Residues in contact with ASN 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ALA* 4.9 0.7 - - + -
113E LEU 3.3 21.1 - - - +
114E SER* 3.4 17.6 + - - +
245E THR 3.3 21.6 + - - -
246E VAL* 3.4 8.0 - - - +
247E LEU* 2.9 31.3 + - - +
255E SER 5.4 1.4 - - - +
257E PRO* 3.6 16.0 - - + +
319E ALA 2.9 21.8 + - - -
320E THR 3.2 6.0 + - - +
322E GLU* 1.3 73.7 - - - +
324E ALA* 1.3 65.5 + - - +
326E LYS* 3.1 9.8 + - - +
327E GLY 2.9 20.3 + - - -
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E VAL* 4.9 1.3 - - + -
112E ALA* 4.0 15.1 - - + +
259E VAL* 3.8 27.4 - - + +
320E THR 2.8 19.8 + - - +
321E MET* 3.6 24.5 - - + +
323E ASN* 1.3 72.0 - - - +
325E GLN* 1.3 63.3 + - + +
327E GLY 3.3 18.9 + - - +
328E GLU 5.3 0.2 - - - -
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Residues in contact with GLN 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E MET* 2.8 31.0 + - + +
322E GLU* 3.6 10.1 + - + +
324E ALA* 1.3 77.4 - - + +
326E LYS* 1.3 61.6 + - + +
327E GLY 3.3 8.3 - - - +
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Residues in contact with LYS 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E VAL* 4.2 31.0 - - + -
247E LEU 5.9 2.0 - - - +
254E PRO* 3.5 34.0 - - + +
255E SER 3.9 15.0 - - - +
256E LYS* 3.6 17.2 - - - +
322E GLU* 3.1 24.0 + - + +
323E ASN* 3.1 10.3 + - - +
325E GLN* 1.3 75.2 - - + +
327E GLY* 1.3 59.0 + - - +
328E GLU* 5.6 0.7 - - - +
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Residues in contact with GLY 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LYS* 3.7 14.6 - - - -
257E PRO* 3.4 19.0 - - - +
323E ASN 2.9 10.2 + - - -
324E ALA 3.3 15.3 - - - +
325E GLN 3.2 9.4 - - - +
326E LYS* 1.3 78.6 - - - +
328E GLU* 1.3 68.5 + - - +
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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