Contacts of the helix formed by residues 336 - 354 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASP 3.0 10.7 - - - +
335B ASP* 1.3 89.8 - - - +
337B VAL* 1.3 65.1 + - + +
339B LYS* 3.7 10.2 - - + +
340B GLN* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ASP* 3.0 12.5 + - - +
336B PRO* 1.3 82.0 - - + +
338B ARG* 1.3 58.0 + - + +
340B GLN* 3.8 7.7 - - - +
341B ARG* 3.0 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.6 24.0 + - - +
289B ASP* 2.8 40.8 + - - -
333B ILE* 3.4 32.3 - - + -
335B ASP* 3.2 27.9 + - - +
337B VAL* 1.3 75.8 - - + +
339B LYS* 1.3 66.9 + - - +
341B ARG* 3.5 21.9 - - - +
342B TYR* 2.9 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.2 32.9 - - + +
331B LYS* 4.7 7.7 + - - +
333B ILE* 3.2 29.5 + - + +
334B ASP* 4.9 8.4 + - - +
335B ASP 2.8 16.0 + - - +
336B PRO* 3.7 10.1 - - + +
337B VAL 3.3 0.2 - - - -
338B ARG* 1.3 77.3 - - - +
340B GLN* 1.3 57.4 + - - +
343B HIS* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PRO 3.1 17.5 + - - +
337B VAL* 3.8 7.5 - - - +
339B LYS* 1.3 77.0 - - - +
341B ARG* 1.3 60.2 + - - +
343B HIS* 4.6 2.9 - - - -
344B ASP* 2.8 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 2.8 32.1 + - - -
292B THR* 3.2 32.5 - - - +
293B VAL* 3.4 28.4 - - + +
337B VAL* 3.0 37.5 + - + +
338B ARG* 3.5 29.9 - - - +
340B GLN* 1.3 77.5 + - - +
342B TYR* 1.3 71.3 + - + +
344B ASP* 4.2 2.8 - - - +
345B PHE* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.4 16.3 + - - -
288B LEU* 3.5 33.9 - - + -
289B ASP* 2.7 28.9 + - - -
292B THR* 4.4 3.6 - - + -
326B ALA* 3.8 26.0 - - + +
329B TYR* 3.6 37.5 - + + -
330B ALA* 4.4 3.6 - - + -
333B ILE* 4.4 5.8 - - + -
338B ARG* 2.9 48.5 + - + +
339B LYS 4.2 1.1 - - - +
341B ARG* 1.3 88.8 - - + +
343B HIS* 1.3 67.3 + - - +
345B PHE* 3.3 7.3 + + - +
346B ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA 5.0 0.2 - - - -
327B LEU* 3.7 22.4 - - + +
330B ALA* 4.1 15.1 - - + +
339B LYS* 3.0 23.2 + - + +
340B GLN* 3.9 3.6 - - - +
342B TYR* 1.3 75.9 - - - +
344B ASP* 1.3 77.2 + - - +
346B ALA* 3.3 4.3 + - - +
347B VAL* 3.2 35.9 + - + +
443B GLU* 2.9 31.1 + - - -
444B TYR* 3.1 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLN* 2.8 45.8 + - - +
341B ARG* 4.2 3.1 - - - +
343B HIS* 1.3 86.3 + - - +
345B PHE* 1.3 64.3 + - - +
347B VAL* 3.6 5.0 + - - +
348B ARG* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 5.2 1.6 - - + -
291B TRP* 3.6 37.9 - + + -
292B THR* 3.7 20.2 - - + -
302B TYR* 3.3 28.7 - - - -
308B ALA* 4.4 1.3 - - + -
319B ALA 4.8 0.7 - - - -
322B THR* 3.6 28.9 - - + -
323B ALA* 4.1 11.7 - - - -
326B ALA* 4.0 8.3 - - + -
341B ARG 3.1 19.3 + - - +
342B TYR* 3.4 7.4 - - - +
344B ASP* 1.3 74.7 - - - +
346B ALA* 1.3 68.1 + - - +
348B ARG* 3.2 7.6 + - - +
349B GLN* 3.0 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA* 3.3 38.3 - - + +
326B ALA* 4.3 2.5 - - + -
327B LEU* 3.5 20.2 - - + -
342B TYR 3.0 12.9 + - - +
343B HIS 3.3 9.4 + - - +
345B PHE* 1.3 78.4 - - - +
347B VAL* 1.3 63.2 + - - +
349B GLN* 3.1 4.5 + - - +
350B ILE* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.3 7.6 - - - +
327B LEU* 4.7 2.0 - - + -
343B HIS* 3.2 39.3 + - + +
344B ASP* 4.0 5.6 - - - +
346B ALA* 1.3 74.5 - - - +
348B ARG* 1.3 59.8 + - - +
350B ILE* 3.4 4.5 + - - +
351B ASN* 2.9 50.4 + - - +
440B LEU* 3.9 24.2 - - + -
444B TYR* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 6.4 0.2 - - + -
305B GLY 2.9 27.8 + - - -
306B GLY* 4.3 7.8 + - - +
344B ASP 3.0 18.3 + - - +
345B PHE* 3.5 7.0 - - - +
347B VAL* 1.3 78.4 - - - +
349B GLN* 1.3 70.7 + - - +
351B ASN* 3.6 3.6 + - - +
352B TYR* 3.0 38.3 + - - +
356B ASP* 3.0 52.4 + - - +
357B ASN* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 4.2 11.9 - - - -
306B GLY 3.0 24.0 + - - -
307B MET* 3.6 7.4 - - - +
308B ALA* 3.0 31.6 + - - +
316B LEU* 5.3 2.6 - - - +
319B ALA* 3.9 30.7 - - + +
320B ALA* 6.2 0.2 - - - -
323B ALA* 4.4 3.8 - - + -
345B PHE* 3.0 41.4 + - + +
346B ALA 3.1 5.6 + - - +
348B ARG* 1.3 84.2 - - - +
350B ILE* 1.3 64.8 + - - +
352B TYR* 3.4 7.2 + - - +
353B ALA* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.6 0.7 - - + -
320B ALA* 4.2 12.8 - - + -
323B ALA* 3.9 16.8 - - + -
327B LEU* 5.7 1.1 - - + -
346B ALA* 3.1 17.7 + - + +
347B VAL 4.1 1.6 - - - +
349B GLN* 1.3 76.1 - - - +
351B ASN* 1.3 64.6 + - - +
353B ALA* 3.1 8.1 + - + +
354B LEU* 3.0 30.0 + - + +
433B PHE* 4.1 21.5 - - + -
436B ALA* 3.7 27.8 - - + -
437B LEU* 4.0 21.1 - - + -
440B LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 4.1 9.7 - - - +
4B PHE* 3.5 28.6 - - + -
6B TYR* 2.7 34.3 + - - -
347B VAL* 2.9 32.5 + - - +
348B ARG* 3.9 8.2 - - - +
350B ILE* 1.3 73.7 - - - +
352B TYR* 1.3 65.1 + - - +
354B LEU* 3.1 3.2 + - - +
355B GLY 3.0 7.4 + - - -
356B ASP* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLY 4.2 7.2 - - - -
306B GLY 4.4 1.6 - - - +
307B MET* 3.6 47.6 - - + -
316B LEU* 4.2 9.4 - - + -
348B ARG* 3.0 31.5 + - - +
349B GLN* 3.5 10.5 - - - +
350B ILE 3.2 0.4 - - - -
351B ASN* 1.3 77.2 - - - +
353B ALA* 1.3 63.2 + - - +
355B GLY 3.2 2.8 + - - -
356B ASP 3.4 22.2 - - - -
357B ASN* 2.9 45.2 + - + +
358B PRO* 4.1 4.2 - - + +
363B TYR* 3.8 23.0 + + - -
406B PRO* 4.1 5.0 - - + +
411B ASP* 2.8 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.3 12.1 - - + -
320B ALA* 6.4 1.1 - - + -
349B GLN 3.3 9.0 + - - +
350B ILE* 3.1 10.8 + - + +
352B TYR* 1.3 81.1 - - - +
354B LEU* 1.3 61.1 + - - +
363B TYR* 2.9 39.9 + - - +
364B VAL* 4.1 4.7 - - - +
402B LEU* 4.1 24.0 - - + -
433B PHE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.5 35.3 - - + -
6B TYR* 3.6 38.4 - - + -
9B ALA* 4.2 9.4 - - + -
350B ILE* 3.0 26.3 + - + +
351B ASN 3.1 6.0 + - - +
353B ALA* 1.3 78.3 - - - +
355B GLY* 1.3 54.3 + - - +
362B SER* 3.8 17.0 - - - +
364B VAL* 3.8 9.6 - - + -
367B PHE* 3.6 27.6 - - + -
368B GLY* 5.1 2.4 - - - -
369B ASN 5.3 1.0 + - - -
433B PHE* 3.8 25.4 - - + -
437B LEU* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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