Contacts of the helix formed by residues 314 - 325 (chain F) in PDB entry 1TYE
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 VAL 314 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262E TRP* 6.1 1.3 - - + +
250F THR 4.3 0.4 - - - +
251F ASP 4.0 11.7 - - - +
252F ALA* 3.8 14.1 - - - +
253F LYS* 3.9 1.8 - - + +
310F VAL* 3.6 19.7 - - + +
311F THR* 3.3 23.1 - - - +
312F GLU 3.1 0.2 - - - -
313F ASN* 1.3 88.3 - - - +
315F VAL* 1.3 62.2 + - - +
316F ASN 3.6 1.8 - - - -
317F LEU* 3.4 34.9 - - + +
318F TYR* 3.1 29.9 + - + -
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Residues in contact with VAL 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F VAL* 3.8 18.2 - - + +
311F THR 3.3 18.4 - - - +
312F GLU* 3.2 21.5 + - + +
313F ASN 3.6 0.4 - - - -
314F VAL* 1.3 73.9 - - - +
316F ASN* 1.3 68.0 + - - +
317F LEU 3.1 1.5 + - - -
318F TYR* 3.2 3.8 + - - +
319F GLN* 2.9 47.9 + - - +
330F VAL* 4.2 9.2 - - + +
332F VAL* 4.0 18.2 - - + +
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Residues in contact with ASN 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F GLU 4.9 0.7 + - - +
313F ASN 5.5 0.4 + - - -
314F VAL 3.6 0.2 - - - -
315F VAL* 1.3 85.2 - - - +
317F LEU* 1.3 62.4 + - - +
319F GLN* 3.5 18.2 + - - +
320F ASN* 3.0 29.8 + - - +
1I NAG 3.4 23.2 + - + +
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Residues in contact with LEU 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E TRP* 3.8 36.6 - - + +
263E THR* 4.7 0.7 - - + +
285E MET* 3.9 11.8 - - + +
253F LYS* 3.5 30.5 - - + -
314F VAL* 3.4 36.9 + - + +
315F VAL 3.1 0.2 - - - -
316F ASN* 1.3 81.6 - - - +
318F TYR* 1.3 69.3 + - + +
320F ASN* 3.3 4.5 + - - +
321F TYR* 3.2 48.3 + - + +
1I NAG 3.2 12.6 - - + +
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Residues in contact with TYR 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 4.6 5.2 - + - -
248F PHE* 4.1 18.4 - + - -
250F THR* 3.4 16.9 + - + +
252F ALA 2.8 20.2 + - - -
254F THR* 3.4 34.7 + - + -
308F PHE* 3.8 34.0 - + + -
310F VAL* 3.6 21.1 - - + -
314F VAL* 3.1 45.8 - - + +
315F VAL 3.2 4.2 + - - +
317F LEU* 1.3 85.7 - - + +
319F GLN* 1.3 64.0 + - - +
321F TYR* 3.2 15.1 + + - +
322F SER* 3.1 22.7 + - - -
330F VAL* 3.5 6.5 - - + +
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Residues in contact with GLN 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F VAL* 2.9 34.7 + - - +
316F ASN* 3.5 21.6 + - - +
317F LEU 3.2 0.2 - - - -
318F TYR* 1.3 76.1 - - - +
320F ASN* 1.3 61.8 + - - +
322F SER* 2.9 27.2 + - - -
323F GLU* 3.1 12.2 - - - +
330F VAL* 3.7 21.3 - - + +
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Residues in contact with ASN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E MET* 3.4 21.5 - - + +
316F ASN* 3.0 14.8 + - - +
317F LEU 3.7 3.1 - - - +
319F GLN* 1.3 79.7 + - - +
321F TYR* 1.3 61.3 + - - +
323F GLU* 3.4 28.5 - - + +
324F LEU* 3.7 15.8 - - - +
1I NAG 1.5 72.1 + - - +
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Residues in contact with TYR 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E THR* 2.9 36.0 + - - +
285E MET* 3.6 24.0 - - + -
286E ALA* 4.7 6.5 - - + -
223F PHE* 4.7 5.8 - + + -
253F LYS* 6.1 0.3 - - - +
254F THR* 3.9 25.1 + - + +
256F ILE* 3.9 10.0 - - + +
292F LEU* 4.3 24.9 - - + +
308F PHE* 4.4 11.9 - - + -
317F LEU* 3.2 37.0 + - + +
318F TYR* 3.4 27.6 - + - +
319F GLN 3.1 0.6 - - - -
320F ASN* 1.3 76.8 - - - +
322F SER* 1.3 63.1 + - - +
324F LEU* 3.5 7.6 + - + +
325F ILE* 3.3 30.8 + - + +
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Residues in contact with SER 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F PHE* 4.2 3.4 - - - -
318F TYR 3.1 13.7 + - - -
319F GLN* 2.9 14.7 + - - -
321F TYR* 1.3 73.5 - - - +
323F GLU* 1.3 61.7 + - - +
324F LEU 3.0 2.0 - - - -
325F ILE 2.6 31.9 + - - +
326F PRO* 3.5 2.3 - - - +
328F THR* 3.1 33.8 + - - -
330F VAL* 3.1 19.9 - - - +
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Residues in contact with GLU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E LEU* 4.1 8.1 - - - +
319F GLN* 3.1 17.9 - - - +
320F ASN* 3.4 27.8 - - - +
322F SER* 1.3 76.5 - - - +
324F LEU* 1.3 65.5 + - + +
325F ILE 3.6 0.8 + - - -
326F PRO* 4.0 14.3 - - - +
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Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E GLN* 4.2 18.6 - - + +
285E MET* 3.7 38.1 - - + +
314E MET* 3.6 32.4 - - + +
322E LEU* 3.8 16.9 - - + +
292F LEU* 3.7 20.7 - - + +
296F THR* 3.9 7.1 + - - +
320F ASN 3.7 17.5 - - - +
321F TYR* 3.5 8.4 + - + +
322F SER 3.0 0.6 - - - -
323F GLU* 1.3 84.5 - - + +
325F ILE* 1.3 61.6 + - - +
326F PRO* 3.4 8.1 - - - +
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Residues in contact with ILE 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 5.5 0.9 - - + -
292F LEU* 4.1 27.6 - - + +
295F MET* 4.2 15.5 - - + -
296F THR* 3.6 24.9 - - + +
299F LEU* 4.0 18.8 - - + -
306F LEU* 4.7 5.4 - - + -
308F PHE* 4.6 20.6 - - + -
321F TYR* 3.3 18.4 + - + +
322F SER 2.6 15.6 + - - +
324F LEU* 1.3 81.5 - - - +
326F PRO* 1.3 63.3 - - - +
328F THR* 2.7 36.8 + - + +
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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