Contacts of the helix formed by residues 333 - 346 (chain A) in PDB entry 5TQW
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 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A LEU* 5.4 1.4 - - - +
331A ASP 3.6 3.2 + - - -
332A GLU* 1.3 83.9 - - - +
334A LEU* 1.3 63.6 + - - +
335A HIS* 3.0 9.5 + - - +
336A SER* 2.7 38.5 + - - -
337A LEU* 3.3 16.8 + - - +
364A PRO 4.4 7.0 - - - -
365A ARG* 5.7 2.5 - - - -
366A LYS 4.3 4.3 - - - -
367A PRO* 4.3 2.2 - - - -
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Residues in contact with LEU 334 (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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333A SER* 1.3 75.5 - - - +
335A HIS* 1.3 57.5 + - - +
337A LEU* 3.2 29.0 + - + +
338A GLN* 2.8 41.5 + - + +
341A ILE* 6.3 0.2 - - + -
354A LEU* 4.9 16.8 - - + -
362A LEU* 3.8 39.7 - - + +
363A ASP 4.0 0.2 - - - +
364A PRO* 3.5 22.0 + - + +
366A LYS 3.1 21.6 + - - +
367A PRO 3.7 13.6 - - - +
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Residues in contact with HIS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 3.0 8.5 + - - +
334A LEU* 1.3 77.4 - - - +
336A SER* 1.3 66.6 + - - +
338A GLN* 2.9 32.6 + - - +
339A SER* 3.0 26.1 + - - -
349A THR* 4.1 15.9 - - + -
364A PRO* 3.7 15.1 + - + +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLU* 3.1 25.8 - - - +
333A SER* 2.7 21.7 + - - -
335A HIS* 1.3 77.6 - - - +
337A LEU* 1.3 58.4 + - - +
339A SER* 2.3 31.6 + - - -
340A ARG* 3.0 10.9 + - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 6.0 6.1 - - + -
315A ILE* 5.4 6.5 - - + -
326A PHE* 3.9 31.9 - - + -
327A LEU 4.8 0.9 - - - +
328A LEU* 4.7 15.0 - - + -
332A GLU* 3.0 12.3 + - - +
333A SER 3.3 10.8 + - - +
334A LEU* 3.2 32.6 + - + +
336A SER* 1.3 77.0 - - - +
338A GLN* 1.3 55.2 + - - +
340A ARG* 3.1 36.3 + - - +
341A ILE* 2.8 35.5 + - + +
354A LEU* 6.4 0.2 - - + -
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 2.8 25.6 + - + +
335A HIS* 2.9 37.2 + - - +
337A LEU* 1.3 73.7 - - - +
339A SER* 1.3 57.7 + - - +
341A ILE* 3.1 11.6 + - + -
342A GLU* 2.9 24.1 + - - +
349A THR* 3.5 22.6 + - + +
352A GLN* 3.2 27.7 + - + +
354A LEU* 4.7 12.2 - - + +
364A PRO* 3.4 29.5 - - - +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 3.0 14.9 + - - -
336A SER* 2.3 31.7 + - - -
338A GLN* 1.3 77.0 - - - +
340A ARG* 1.3 57.6 + - - +
342A GLU* 3.2 10.6 + - - +
343A ARG* 2.9 26.9 + - - +
349A THR* 4.6 4.9 + - - +
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Residues in contact with ARG 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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326A PHE* 4.1 14.6 - - + +
327A LEU* 2.4 49.9 + - - +
329A PRO* 3.7 5.8 - - - +
332A GLU* 3.1 35.4 + - - +
336A SER 3.0 13.1 + - - +
337A LEU* 3.1 27.4 + - + +
339A SER* 1.3 76.6 + - - +
341A ILE* 1.3 59.4 + - - +
343A ARG* 3.8 27.4 - - - +
344A GLU* 2.8 37.4 + - + +
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Residues in contact with ILE 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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315A ILE* 4.4 11.7 - - + -
326A PHE* 3.5 25.6 - - + -
334A LEU* 6.3 0.4 - - + -
337A LEU* 2.8 25.9 + - + +
338A GLN* 3.1 12.5 + - + +
340A ARG* 1.3 76.8 - - - +
342A GLU* 1.3 56.5 + - - +
345A THR* 2.3 56.8 + - + +
352A GLN* 3.4 30.1 - - + +
354A LEU* 3.9 31.6 - - + -
386A LEU* 4.3 13.2 - - + -
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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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338A GLN 2.9 9.2 + - - +
339A SER* 3.2 10.7 + - - +
341A ILE* 1.3 75.9 - - - +
343A ARG* 1.3 57.9 + - - +
346A GLY* 3.2 23.4 + - - -
347A ILE 3.3 26.2 - - - +
348A ASN* 3.0 28.3 - - - +
349A THR* 2.7 18.3 + - - -
352A GLN* 3.2 5.1 - - - +
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Residues in contact with ARG 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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339A SER 2.9 15.8 + - - +
340A ARG* 3.4 25.4 + - - +
342A GLU* 1.3 80.7 - - - +
344A GLU* 1.3 97.9 + - - +
345A THR 3.5 0.9 + - - -
346A GLY* 4.2 2.3 + - - -
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Residues in contact with GLU 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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324A ILE* 4.4 11.2 - - + +
326A PHE* 3.9 29.5 - - + -
340A ARG* 2.8 22.3 + - + +
343A ARG* 1.3 119.3 + - - +
345A THR* 1.3 62.1 + - - +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 6.5 0.4 - - + -
317A ASN* 4.8 13.6 + - + +
324A ILE* 4.2 18.8 - - + -
326A PHE* 4.7 5.2 - - + -
341A ILE* 2.3 47.5 + - + +
343A ARG 4.7 0.2 - - - -
344A GLU* 1.3 87.9 - - + +
346A GLY* 1.3 58.2 + - - +
347A ILE* 3.4 23.5 + - - +
386A LEU* 4.6 10.1 - - + -
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Residues in contact with GLY 346 (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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342A GLU* 3.2 21.9 + - - +
343A ARG 4.2 2.5 + - - -
345A THR* 1.3 77.4 + - - +
347A ILE* 1.3 65.7 + - - +
348A ASN* 3.8 1.9 + - - +
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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