Contacts of the helix formed by residues 336 - 354 (chain A) in PDB entry 1TF4
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 PRO 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ASP 3.0 11.4 - - - +
335A ASP* 1.3 90.2 - - - +
337A VAL* 1.3 64.3 + - + +
339A LYS* 3.7 9.8 - - + +
340A GLN* 3.1 25.3 + - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 3.0 11.8 + - - +
336A PRO* 1.3 82.4 - - + +
338A ARG* 1.3 58.5 + - + +
340A GLN* 3.8 7.9 - - - +
341A ARG* 3.0 51.1 + - + +
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.6 22.8 + - - +
289A ASP* 3.0 30.7 + - - -
333A ILE* 3.4 31.2 - - + -
335A ASP* 3.2 29.3 + - + +
337A VAL* 1.3 74.9 - - + +
339A LYS* 1.3 66.3 + - - +
341A ARG* 3.5 22.3 - - - +
342A TYR* 2.9 57.6 + - + +
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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
----------------------------------------------------------
330A ALA* 3.2 32.7 - - + +
331A LYS* 4.7 7.6 + - - +
333A ILE* 3.2 29.7 + - + +
334A ASP* 4.9 9.2 + - - +
335A ASP 2.9 17.0 + - - +
336A PRO* 3.7 9.6 - - + +
338A ARG* 1.3 76.0 - - - +
340A GLN* 1.3 63.6 + - - +
343A HIS* 3.0 28.8 + - + +
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO 3.1 17.9 + - - +
337A VAL* 3.8 7.1 - - - +
339A LYS* 1.3 79.5 - - - +
341A ARG* 1.3 57.7 + - - +
343A HIS* 4.6 2.9 - - - -
344A ASP* 2.8 56.8 + - - +
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASP* 2.8 26.3 + - - -
292A THR* 3.3 33.5 - - - +
293A VAL* 3.5 27.3 - - + +
337A VAL* 3.0 38.7 + - + +
338A ARG* 3.5 30.8 - - - +
340A GLN* 1.3 77.3 + - - +
342A TYR* 1.3 71.3 + - + +
344A ASP* 4.1 3.0 - - - +
345A PHE* 3.1 23.9 + - - +
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Residues in contact with TYR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.4 16.3 + - - -
288A LEU* 3.5 33.0 - - + -
289A ASP* 2.8 28.1 + - - -
292A THR* 4.5 3.4 - - + -
326A ALA* 3.8 25.8 - - + +
329A TYR* 3.6 37.5 - + + -
330A ALA* 4.4 3.4 - - + -
333A ILE* 4.5 6.1 - - + -
338A ARG* 2.9 47.7 + - + +
339A LYS 4.2 1.8 - - - +
341A ARG* 1.3 90.3 - - + +
343A HIS* 1.3 67.1 + - - +
345A PHE* 3.3 6.8 + + - +
346A ALA* 3.1 23.4 + - - +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA 5.0 0.4 - - - -
327A LEU* 3.7 22.8 - - + +
330A ALA* 4.0 16.1 - - + +
339A LYS* 3.0 22.6 + - + +
340A GLN* 3.9 3.6 - - - +
342A TYR* 1.3 77.5 - - - +
344A ASP* 1.3 76.1 + - - +
346A ALA* 3.3 4.3 + - - +
347A VAL* 3.2 36.4 + - + +
443A GLU* 2.9 32.2 + - - -
444A TYR* 3.2 24.2 - - - -
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLN* 2.8 44.8 + - - +
341A ARG* 4.2 3.1 - - - +
343A HIS* 1.3 86.4 + - - +
345A PHE* 1.3 65.0 + - - +
347A VAL* 4.0 5.1 - - - +
348A ARG* 3.1 24.8 + - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 5.2 2.0 - - + -
291A TRP* 3.7 38.1 - + + -
292A THR* 3.7 19.7 - - + -
302A TYR* 3.4 26.9 - - - -
308A ALA* 4.4 1.1 - - + -
319A ALA 4.8 0.9 - - - -
322A THR* 3.6 28.7 - - + -
323A ALA* 4.1 11.7 - - - -
326A ALA* 4.0 8.3 - - + -
341A ARG 3.1 19.4 + - - +
342A TYR* 3.4 8.3 - + - +
344A ASP* 1.3 76.5 - - - +
346A ALA* 1.3 67.3 + - - +
348A ARG* 3.2 6.3 + - - +
349A GLN* 3.0 48.9 + - + +
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Residues in contact with ALA 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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323A ALA* 3.3 39.4 - - + +
326A ALA* 4.2 2.2 - - + -
327A LEU* 3.5 20.0 - - + -
342A TYR 3.1 9.6 + - - +
343A HIS 3.5 8.7 - - - +
345A PHE* 1.3 82.6 - - - +
347A VAL* 1.3 63.1 + - - +
349A GLN* 3.1 4.0 + - - +
350A ILE* 3.1 28.3 + - - +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 4.3 8.1 - - - +
327A LEU* 4.7 2.0 - - + -
343A HIS* 3.2 40.4 + - + +
344A ASP* 4.1 5.6 - - - +
346A ALA* 1.3 75.1 - - - +
348A ARG* 1.3 57.8 + - - +
350A ILE* 4.0 5.0 - - - +
351A ASN* 2.9 50.8 + - - +
440A LEU* 3.9 24.5 - - + -
444A TYR* 4.0 13.5 - - + +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 6.4 0.2 - - + -
305A GLY 2.9 28.3 + - - -
306A GLY* 4.3 8.4 + - - +
344A ASP 3.1 19.0 + - - +
345A PHE* 3.5 7.0 - - - +
347A VAL* 1.3 78.2 - - - +
349A GLN* 1.3 69.6 + - - +
351A ASN* 4.2 4.5 - - - +
352A TYR* 3.0 38.6 + - - +
356A ASP* 3.0 50.4 + - - -
357A ASN* 4.7 1.2 - - - +
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 4.1 11.5 - - - -
306A GLY 3.1 23.2 + - - -
307A MET* 3.7 7.0 - - - +
308A ALA* 2.9 33.4 + - - +
316A LEU* 5.3 2.9 - - - +
319A ALA* 3.9 29.5 - - + +
320A ALA* 6.2 0.2 - - - -
323A ALA* 4.4 3.6 - - + -
345A PHE* 3.0 43.2 + - + +
346A ALA 3.1 4.0 + - - +
348A ARG* 1.3 84.7 + - - +
350A ILE* 1.3 65.7 + - + +
352A TYR* 3.4 7.6 + - - +
353A ALA* 3.3 18.7 + - - +
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Residues in contact with ILE 350 (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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6A TYR* 4.6 0.4 - - + -
320A ALA* 4.3 12.1 - - + -
323A ALA* 3.9 17.3 - - + -
327A LEU* 5.7 1.1 - - + -
346A ALA* 3.1 17.2 + - + +
347A VAL 4.1 1.3 - - - +
349A GLN* 1.3 76.0 - - - +
351A ASN* 1.3 63.7 + - - +
353A ALA* 3.1 8.0 + - + +
354A LEU* 3.0 30.2 + - + +
433A PHE* 4.1 22.2 - - + -
436A ALA* 3.7 26.7 - - + -
437A LEU* 4.0 21.3 - - + -
440A LEU* 3.8 28.5 - - + -
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Residues in contact with ASN 351 (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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3A ALA* 4.1 10.1 - - - +
4A PHE* 3.5 28.9 - - + -
6A TYR* 2.7 34.4 + - - -
347A VAL* 2.9 32.8 + - - +
348A ARG* 3.9 7.7 - - - +
350A ILE* 1.3 73.2 - - - +
352A TYR* 1.3 64.5 + - - +
354A LEU* 3.1 2.7 + - - +
355A GLY 3.1 8.0 + - - -
356A ASP* 2.8 34.8 + - + +
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Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLY 4.0 7.6 - - - -
306A GLY 4.4 1.3 - - - +
307A MET* 3.5 49.8 - - + +
316A LEU* 4.2 10.5 - - + -
348A ARG* 3.0 29.7 + - - +
349A GLN* 3.5 11.9 - - - +
350A ILE 3.2 0.2 - - - -
351A ASN* 1.3 77.0 - - - +
353A ALA* 1.3 62.1 + - - +
355A GLY 3.3 2.3 + - - -
356A ASP 3.4 21.1 - - - -
357A ASN* 2.8 46.9 + - + +
358A PRO* 4.1 0.4 - - + -
363A TYR* 3.8 23.8 + + - -
406A PRO* 4.1 5.1 - - + +
411A ASP* 2.8 43.1 + - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.3 12.3 - - + +
320A ALA* 6.4 1.1 - - + -
349A GLN 3.3 8.1 + - - +
350A ILE* 3.1 11.5 + - + +
352A TYR* 1.3 81.8 - - - +
354A LEU* 1.3 60.2 + - - +
363A TYR* 2.9 39.1 + - - +
364A VAL* 4.1 4.6 - - - +
402A LEU* 4.1 24.0 - - + -
433A PHE* 4.3 12.3 - - + -
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Residues in contact with LEU 354 (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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4A PHE* 3.5 34.5 - - + -
6A TYR* 3.6 37.7 - - + -
9A ALA* 4.2 9.4 - - + -
350A ILE* 3.0 27.0 + - + +
351A ASN 3.1 6.0 + - - +
353A ALA* 1.3 77.8 - - - +
355A GLY* 1.3 55.2 + - - +
362A SER* 3.8 16.2 - - - -
364A VAL* 3.8 21.8 - - + -
367A PHE* 3.6 27.6 - - + -
368A GLY* 5.1 2.4 - - - -
369A ASN 5.3 0.9 + - - -
433A PHE* 3.8 14.1 - - + -
437A LEU* 4.3 4.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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