Contacts of the helix formed by residues 353 - 367 (chain A) in PDB entry 1TQN
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 MET 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLU* 3.0 19.5 - - + +
335A ILE* 4.1 22.4 - - - -
338A VAL* 3.7 22.4 - - + -
339A LEU* 4.1 10.1 - - + -
349A THR* 3.0 42.4 - - + +
350A VAL* 3.0 12.5 + - - +
351A LEU 3.3 3.6 - - - +
352A GLN* 1.3 75.4 - - - +
354A GLU* 1.3 59.8 + - - +
356A LEU* 3.7 10.7 - - + +
357A ASP* 3.3 23.9 + - - +
453A LYS* 5.2 0.9 + - - -
457A ILE* 3.3 41.1 - - + -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 3.4 6.8 + - - +
351A LEU 5.7 1.8 - - - +
352A GLN 3.3 9.3 + - - +
353A MET* 1.3 70.7 - - - +
355A TYR* 1.3 61.7 + - - +
356A LEU 3.1 1.1 - - - -
357A ASP* 3.2 7.1 + - + +
358A MET* 2.8 38.8 + - + +
421A LYS* 3.1 54.4 + - - +
424A LYS* 5.5 3.3 + - - -
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Residues in contact with TYR 355 (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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327A VAL* 3.3 60.5 - - + +
330A LYS* 3.5 47.8 - - + +
331A LEU* 3.7 15.9 - - + -
334A GLU* 2.8 27.1 + - + +
354A GLU* 1.3 74.2 - - - +
356A LEU* 1.3 64.0 + - - +
358A MET* 3.1 20.7 + - + +
359A VAL* 2.8 31.2 + - + +
416A PRO* 4.1 18.5 - - + +
417A GLU* 3.9 16.3 + - - -
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Residues in contact with LEU 356 (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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331A LEU* 3.8 36.0 - - + +
334A GLU* 3.0 14.0 + - - +
335A ILE* 5.4 0.7 - - + -
350A VAL 4.8 2.9 - - - +
353A MET* 3.7 18.4 - - + +
355A TYR* 1.3 75.6 - - - +
357A ASP* 1.3 64.5 + - - +
359A VAL* 3.0 5.8 + - + +
360A VAL* 3.0 26.0 + - + +
453A LYS* 3.5 38.8 - - + -
456A LEU* 4.2 28.9 - - + -
457A ILE* 3.8 27.8 - - + +
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU 6.0 0.7 - - - +
353A MET 3.3 11.9 + - - +
354A GLU* 3.2 12.3 + - + +
356A LEU* 1.3 79.4 - - - +
358A MET* 1.3 56.9 + - - +
360A VAL* 3.6 2.0 + - - +
361A ASN* 3.1 57.4 + - - +
424A LYS* 5.2 8.5 + - - +
449A LEU* 5.7 3.8 - - - +
453A LYS* 2.7 35.7 + - - +
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Residues in contact with MET 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS* 5.8 0.4 - - - +
354A GLU* 2.8 26.4 + - + +
355A TYR* 3.4 26.5 - - + +
357A ASP* 1.3 74.9 - - + +
359A VAL* 1.3 59.0 + - - +
361A ASN* 3.9 1.4 - - - +
362A GLU* 2.9 32.4 + - - +
416A PRO* 3.4 30.2 - - + +
417A GLU* 3.4 33.0 - - - +
419A PHE* 3.6 30.2 - - - +
420A SER* 3.5 20.4 - - - -
421A LYS 4.9 1.1 - - - -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.0 19.7 - - + -
321A LEU* 3.9 20.6 - - + -
327A VAL* 3.7 25.6 - - + -
331A LEU* 4.1 16.2 - - + -
355A TYR* 2.8 30.7 + - + +
356A LEU* 3.5 7.9 - - + +
358A MET* 1.3 73.6 - - - +
360A VAL* 1.3 62.3 + - + +
362A GLU* 3.4 2.1 + - - +
363A THR* 2.8 33.3 + - - -
414A PHE* 4.0 13.3 - - + -
416A PRO* 4.4 7.6 - - + -
456A LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.2 14.0 - - + +
356A LEU* 3.0 17.1 + - + +
357A ASP* 3.7 8.7 - - - +
359A VAL* 1.3 76.5 - - + +
361A ASN* 1.3 60.3 + - - +
363A THR* 3.2 5.7 + - - -
364A LEU* 3.0 37.7 + - + +
449A LEU* 3.8 28.0 - - + -
452A MET* 4.5 10.8 - - + -
453A LYS* 4.2 22.9 - - + +
456A LEU* 4.0 26.7 - - + -
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Residues in contact with ASN 361 (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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357A ASP* 3.1 39.8 + - - +
358A MET 3.9 0.9 - - - +
360A VAL* 1.3 84.3 - - - +
362A GLU* 1.3 62.9 + - - +
364A LEU* 3.1 4.8 + - - +
365A ARG* 2.9 13.0 + - - +
419A PHE* 3.6 36.0 - - + +
424A LYS* 6.4 0.2 - - - +
432A TYR* 2.7 37.0 + - - +
449A LEU* 5.0 5.9 - - - +
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Residues in contact with GLU 362 (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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358A MET 2.9 16.1 + - - +
359A VAL 3.8 0.2 - - - +
360A VAL 3.3 0.2 - - - -
361A ASN* 1.3 75.9 - - - +
363A THR* 1.3 62.6 - - - +
365A ARG* 2.8 38.1 + - - +
366A LEU* 3.1 22.3 + - - +
413A LYS 3.5 0.5 - - - +
414A PHE* 3.6 20.4 - - + -
415A LEU 3.1 40.0 + - - +
416A PRO* 3.4 8.5 - - + -
418A ARG* 3.0 24.0 + - - -
419A PHE* 3.1 21.8 - - + -
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Residues in contact with THR 363 (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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313A VAL* 4.4 4.5 - - + +
316A PHE* 3.5 19.7 - - + +
317A ILE* 3.4 48.5 - - + +
320A GLU* 4.3 3.3 - - + +
359A VAL 2.8 16.2 + - - -
360A VAL 3.5 7.0 - - - -
362A GLU* 1.3 76.7 - - - +
364A LEU* 1.3 58.9 + - - +
366A LEU* 3.1 5.7 + - - +
367A PHE* 2.7 34.2 + - + -
414A PHE* 3.5 16.7 - - - -
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 3.9 33.9 - - + -
360A VAL* 3.0 33.5 + - + +
361A ASN* 3.1 3.3 + - - +
363A THR* 1.3 77.2 - - - +
365A ARG* 1.3 61.4 + - - +
367A PHE 3.8 11.9 - - - +
368A PRO* 3.2 27.7 - - + +
402A HIS* 3.5 3.5 + - - -
432A TYR* 3.5 20.9 - - - +
434A PRO* 3.8 11.3 - - + +
435A PHE* 3.9 29.2 - - + -
449A LEU* 4.5 2.5 - - + -
452A MET* 4.7 4.0 - - + -
508A HEM 4.4 14.8 - - + -
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Residues in contact with ARG 365 (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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361A ASN 2.9 6.9 + - - +
362A GLU* 2.8 38.4 + - - +
363A THR 3.1 0.4 - - - -
364A LEU* 1.3 78.6 - - - +
366A LEU* 1.3 80.4 + - - +
368A PRO* 3.6 2.3 - - - +
402A HIS* 3.1 65.9 + - + +
403A ARG* 4.4 3.4 + - - +
408A TRP* 3.4 38.5 - - + +
411A PRO* 2.7 34.1 + - - +
413A LYS 2.6 30.3 + - - -
418A ARG* 3.2 12.9 - - - +
419A PHE* 4.3 0.9 - - + -
432A TYR* 3.6 15.2 - - + -
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Residues in contact with LEU 366 (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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320A GLU* 4.1 12.6 - - + +
362A GLU 3.1 6.1 + - - +
363A THR* 3.1 3.7 + - - +
365A ARG* 1.3 106.6 - - - +
367A PHE* 1.3 77.5 + - + +
368A PRO* 3.4 5.8 - - - +
399A TYR* 3.5 2.8 - - - -
403A ARG* 2.9 48.0 + - - +
411A PRO 3.6 12.6 - - - +
412A GLU 4.1 11.2 - - - +
414A PHE* 3.8 47.8 - - + +
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Residues in contact with PHE 367 (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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313A VAL* 5.1 0.5 - - - +
316A PHE* 3.5 64.3 - + + -
319A TYR* 5.8 0.4 - + - -
320A GLU* 3.2 28.9 - - + -
363A THR* 2.7 24.5 + - + +
364A LEU* 3.5 17.3 - - - +
366A LEU* 1.3 90.0 - - + +
368A PRO* 1.3 59.9 - - - +
369A ILE* 2.9 14.8 + - - +
403A ARG* 3.7 19.3 - - - -
475A LEU* 4.8 12.1 - - + -
477A LEU* 4.0 21.1 - - + -
483A LEU* 3.7 10.3 - - + -
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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