Contacts of the helix formed by residues 337 - 349 (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 SER 337 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133F ASN* 3.3 23.6 + - - -
134F LEU* 4.4 14.4 - - - +
137F LYS* 3.6 24.7 + - - +
334F SER 5.3 1.4 + - - -
335F MET 3.7 0.6 + - - -
336F ASP* 1.3 73.4 + - - +
338F SER* 1.3 65.4 + - - +
339F ASN 3.5 0.9 - - - -
340F VAL* 3.3 4.5 + - - +
341F LEU* 2.8 53.0 + - - +
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Residues in contact with SER 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F ASP* 2.9 30.4 + - - -
337F SER* 1.3 76.6 - - - +
339F ASN* 1.3 63.7 + - - +
341F LEU* 3.8 4.9 - - - +
342F GLN* 3.0 30.2 + - - +
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Residues in contact with ASN 339 (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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330F VAL 4.3 2.3 + - - +
331F GLY* 3.2 23.2 - - - -
332F VAL* 3.5 35.9 - - + +
336F ASP 4.4 3.6 + - - +
337F SER 3.5 0.2 - - - -
338F SER* 1.3 80.0 - - - +
340F VAL* 1.3 63.4 + - - +
342F GLN* 3.6 15.1 + - - +
343F LEU* 3.8 11.1 + - - +
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Residues in contact with VAL 340 (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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134F LEU* 3.7 33.0 - - + -
138F LEU* 5.1 4.0 - - + -
247F VAL* 4.6 9.0 - - + -
307F ILE* 5.1 8.4 - - + +
309F ALA* 3.9 19.7 - - + -
331F GLY* 4.3 11.7 - - - +
332F VAL 3.4 29.6 - - - +
333F LEU* 4.2 8.7 - - + -
336F ASP 5.0 4.5 - - - +
337F SER* 3.3 5.0 + - - +
339F ASN* 1.3 76.2 - - - +
341F LEU* 1.3 65.0 + - + +
343F LEU* 3.3 18.8 + - - +
344F ILE* 3.7 9.1 + - + +
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Residues in contact with LEU 341 (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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134F LEU* 3.8 15.3 - - + -
137F LYS* 3.8 25.8 - - + +
138F LEU* 3.7 25.6 - - + -
141F GLN* 3.9 34.2 - - + +
337F SER* 2.8 38.9 + - - +
338F SER* 3.8 3.8 - - - +
340F VAL* 1.3 75.8 - - - +
342F GLN* 1.3 59.1 + - - +
344F ILE* 2.9 29.4 + - + +
345F VAL* 3.2 11.2 + - - +
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Residues in contact with GLN 342 (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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338F SER 3.0 20.6 + - - +
339F ASN* 3.8 9.2 - - - +
340F VAL 3.3 0.4 - - - -
341F LEU* 1.3 76.0 - - - +
343F LEU* 1.3 58.0 + - + +
345F VAL* 3.2 20.3 + - - +
346F ASP* 2.9 58.0 + - - +
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Residues in contact with LEU 343 (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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307F ILE* 4.0 32.4 - - + +
329F THR* 4.1 24.8 + - + +
330F VAL 3.7 9.4 - - - +
331F GLY* 3.6 36.6 - - - +
339F ASN* 3.8 11.4 + - - +
340F VAL* 3.3 9.8 + - - +
341F LEU 3.1 0.8 - - - -
342F GLN* 1.3 76.5 - - + +
344F ILE* 1.3 61.2 + - - +
346F ASP* 3.9 17.8 - - + +
347F ALA* 3.3 21.8 + - - +
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Residues in contact with ILE 344 (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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114F ILE* 4.4 5.2 - - + -
138F LEU* 4.0 26.5 - - + -
141F GLN* 4.7 10.1 - - + -
142F MET* 3.1 42.2 - - + +
245F LEU* 4.0 21.9 - - + +
247F VAL* 4.4 13.0 - - + -
307F ILE* 4.1 16.2 - - + -
340F VAL* 3.9 11.4 - - + +
341F LEU* 2.9 16.7 + - + +
343F LEU* 1.3 77.9 - - - +
345F VAL* 1.3 62.8 + - - +
347F ALA* 3.3 6.8 - - - +
348F TYR* 3.2 19.8 + - - +
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Residues in contact with VAL 345 (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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141F GLN* 3.3 32.8 - - + +
145F LEU* 4.4 21.5 - - + -
341F LEU 3.5 12.3 - - - +
342F GLN* 3.2 24.2 + - - +
344F ILE* 1.3 72.9 - - - +
346F ASP* 1.3 68.1 + - - +
347F ALA 3.0 1.8 - - - -
348F TYR* 3.0 13.0 + - - +
349F GLY* 3.0 11.3 + - - -
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Residues in contact with ASP 346 (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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342F GLN* 2.9 40.8 + - - +
343F LEU* 4.1 19.2 - - + +
345F VAL* 1.3 77.4 - - - +
347F ALA* 1.3 59.6 + - - +
349F GLY* 3.6 7.2 + - - +
350F LYS* 3.4 36.1 + - - +
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Residues in contact with ALA 347 (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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245F LEU* 4.3 26.7 - - + -
305F ASN* 6.2 1.1 - - - +
307F ILE* 5.2 2.7 - - + -
343F LEU 3.3 13.8 + - - +
344F ILE* 3.3 13.2 - - - +
345F VAL 3.0 0.2 - - - -
346F ASP* 1.3 78.3 - - - +
348F TYR* 1.3 63.7 + - - +
350F LYS* 3.1 23.0 + - - +
351F ILE* 3.5 11.9 - - - +
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Residues in contact with TYR 348 (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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109F ASP* 4.2 3.5 + - - +
110F TYR* 3.5 50.4 + + + +
112F VAL* 4.0 11.2 - - + -
142F MET* 4.2 10.3 - - + -
145F LEU* 3.2 53.8 + - + -
146F THR* 3.5 21.4 - - + -
344F ILE 3.2 9.0 + - - +
345F VAL 3.0 8.8 + - - +
347F ALA* 1.3 73.1 - - - +
349F GLY* 1.3 60.4 + - - +
350F LYS 3.0 9.8 + - - -
351F ILE* 3.2 32.3 + - + +
352F ARG* 4.4 0.7 + - - -
391F ILE* 4.1 15.7 - - + +
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Residues in contact with GLY 349 (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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345F VAL 3.0 14.1 + - - -
346F ASP* 3.6 4.7 + - - -
347F ALA 3.2 0.6 - - - -
348F TYR* 1.3 75.5 - - - +
350F LYS* 1.3 62.5 + - - +
352F ARG* 2.9 26.2 + - - -
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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