Contacts of the helix formed by residues 334 - 345 (chain A) in PDB entry 1TFZ
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A GLY 5.1 2.5 - - - -
332A VAL 4.4 0.2 - - - -
333A LEU* 1.3 78.1 - - - +
335A ASP* 1.3 67.8 + - - +
336A ASP* 3.5 14.5 + - - +
337A GLN* 3.0 37.1 + - - +
338A ILE* 3.0 20.9 + - - +
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LYS* 3.5 37.5 - - - +
333A LEU 5.4 0.2 - - - +
334A SER* 1.3 74.9 - - - +
336A ASP* 1.3 62.5 + - - +
338A ILE* 3.4 10.4 + - - +
339A LYS* 3.0 46.8 + - - +
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A SER* 3.1 13.9 + - - +
335A ASP* 1.3 81.7 + - - +
337A GLN* 1.3 63.4 + - + +
339A LYS* 3.3 17.3 + - - +
340A GLU* 3.1 24.9 + - - +
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Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.5 18.5 - - + -
332A VAL 3.9 3.6 - - - +
333A LEU* 3.2 29.4 - - + +
334A SER* 3.0 36.4 + - - +
336A ASP* 1.3 78.0 - - + +
338A ILE* 1.3 56.6 + - - +
340A GLU* 3.6 7.3 + - - +
341A CYS* 3.1 32.4 + - - -
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A TYR* 3.9 25.9 - - + +
325A LEU* 4.1 22.0 - - + +
326A LYS* 3.7 36.6 - - + -
329A VAL* 4.5 7.0 - - + -
330A GLY* 4.8 3.6 - - - -
333A LEU* 3.7 26.0 - - + +
334A SER 3.0 21.7 + - - +
335A ASP* 3.6 9.4 - - - +
336A ASP 3.1 0.2 - - - -
337A GLN* 1.3 76.0 - - - +
339A LYS* 1.3 61.7 + - + +
340A GLU 3.2 0.4 - - - -
341A CYS* 3.3 9.1 + - - +
342A GLU* 3.0 24.9 + - - +
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Residues in contact with LYS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ASP* 3.0 35.9 + - - +
336A ASP* 3.3 15.6 + - - +
338A ILE* 1.3 78.8 - - + +
340A GLU* 1.3 58.5 + - - +
342A GLU* 3.1 16.8 + - - +
343A GLU* 2.9 40.2 + - - +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.3 35.6 - - + +
300A ARG* 3.2 26.4 + - - -
336A ASP 3.1 17.3 + - - +
337A GLN* 3.7 8.8 - - - +
338A ILE 3.2 0.2 - - - -
339A LYS* 1.3 74.3 - - - +
341A CYS* 1.3 62.1 + - - +
343A GLU* 3.8 19.3 - - - +
344A LEU* 3.3 30.5 + - + +
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Residues in contact with CYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.6 22.2 - - - -
322A TYR* 3.6 8.5 + - + -
325A LEU* 4.9 0.4 - - + -
333A LEU* 4.2 20.2 - - - -
337A GLN 3.1 24.8 + - - -
338A ILE* 3.5 10.8 - - - +
340A GLU* 1.3 76.7 - - - +
342A GLU* 1.3 57.7 + - - +
344A LEU 3.5 0.3 + - - -
345A GLY* 2.9 8.1 + - - -
346A ILE* 2.8 51.7 + - + +
348A VAL* 4.2 13.5 - - + -
357A LEU* 4.5 5.4 - - - -
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A SER* 5.3 3.1 + - - -
319A PRO* 3.7 27.8 - - - +
322A TYR* 3.5 45.8 - - + +
338A ILE* 3.0 10.9 + - - +
339A LYS* 3.3 18.6 - - - +
341A CYS* 1.3 75.6 - - - +
343A GLU* 1.3 66.2 + - + +
345A GLY* 3.4 9.5 + - - -
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Residues in contact with GLU 343 (chain A).
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* 4.8 5.0 + - - -
339A LYS* 2.9 26.3 + - + +
340A GLU* 3.8 23.6 - - - +
341A CYS 3.4 0.2 - - - -
342A GLU* 1.3 77.4 - - + +
344A LEU* 1.3 67.3 + - + +
345A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.3 42.4 - - + +
299A LEU* 4.0 9.1 - - + +
300A ARG* 3.7 35.9 - - + +
303A ARG* 2.9 36.2 + - - +
340A GLU* 3.3 23.8 + - + +
342A GLU 3.2 0.4 - - - -
343A GLU* 1.3 85.2 - - + +
345A GLY* 1.3 62.0 + - - +
346A ILE* 3.3 19.0 + - + +
359A ILE* 3.2 8.5 - - - +
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Residues in contact with GLY 345 (chain A).
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* 4.1 2.5 - - - -
316A SER* 3.8 26.1 + - - -
317A PRO* 3.7 9.7 - - - +
322A TYR* 3.2 12.8 + - - -
341A CYS 2.9 5.8 + - - -
342A GLU 3.4 8.6 + - - -
343A GLU 3.4 0.6 + - - -
344A LEU* 1.3 78.0 - - - +
346A ILE* 1.3 62.6 + - - +
347A LEU* 3.6 7.6 + - - +
359A ILE* 3.4 12.4 - - - +
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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