Contacts of the helix formed by residues 315 - 332 (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 ALA 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.5 15.7 - - + +
308A ALA 4.4 2.8 - - - +
309A VAL* 4.5 6.7 - - + -
310A LEU 5.3 1.6 + - - +
311A ASP 3.5 23.1 - - - +
312A THR 4.5 1.5 + - - +
313A TRP 3.2 2.6 - - - -
314A GLY* 1.3 75.8 - - - +
316A LEU* 1.3 62.6 + - - +
318A TYR* 3.2 9.2 + - - +
319A ALA* 3.1 21.3 + - - +
404A GLY 3.5 6.9 + - - +
406A PRO 3.2 28.0 - - - +
407A GLY* 4.6 1.8 - - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.9 26.0 - - + -
315A ALA* 1.3 75.7 - - - +
317A ARG* 1.3 59.5 - - - +
319A ALA* 3.8 7.5 - - + +
320A ALA* 2.8 32.4 + - - +
349A GLN 5.3 3.1 - - - +
352A TYR* 4.2 16.6 - - + -
353A ALA* 4.3 13.5 - - + -
363A TYR* 3.5 40.2 - - + -
402A LEU* 4.2 15.7 - - + +
403A VAL 3.8 17.9 - - - +
404A GLY 3.1 12.1 + - - +
405A GLY* 3.8 13.0 - - - -
406A PRO* 4.5 0.9 - - + -
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 4.6 2.2 - - - +
260A TRP* 3.7 22.0 - - - +
313A TRP* 3.1 30.7 + - - +
314A GLY* 3.0 20.0 + - - +
316A LEU* 1.3 76.5 - - - +
318A TYR* 1.3 86.3 + - - +
320A ALA* 3.4 2.7 + - - +
321A ASN* 2.8 52.2 + - - +
402A LEU* 4.3 11.2 - - + +
403A VAL 5.1 1.2 + - - -
428A ASP* 2.7 47.8 + - - +
429A TYR* 3.6 50.1 + - + +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TRP* 3.7 32.3 + + - -
257A THR* 3.4 19.5 - - + +
258A ILE 4.9 0.2 - - - -
259A ALA* 3.9 19.5 - - + -
260A TRP* 5.4 3.5 + - - -
291A TRP* 4.3 1.3 - - + -
310A LEU* 3.7 26.7 - - + -
311A ASP* 3.9 25.1 + - + -
313A TRP* 3.1 29.0 - - + +
314A GLY 2.9 12.0 + - - -
315A ALA* 3.5 8.1 - - - +
317A ARG* 1.3 100.8 + - - +
319A ALA* 1.3 63.0 + - - +
321A ASN* 3.2 4.6 + - - +
322A THR* 3.0 28.2 + - - -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TRP* 4.1 13.9 - - + -
307A MET* 5.4 1.3 - - + -
308A ALA 3.9 17.7 + - - +
315A ALA 3.1 12.7 + - - +
316A LEU* 3.8 15.3 - - + +
318A TYR* 1.3 75.8 - - - +
320A ALA* 1.3 57.9 + - - +
322A THR* 3.4 3.6 + - - -
323A ALA* 2.9 28.8 + - - +
345A PHE* 4.8 0.2 - - - -
349A GLN* 3.9 31.1 - - + +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU 2.8 18.5 + - - +
317A ARG* 3.6 7.0 - - - +
319A ALA* 1.3 75.1 - - - +
321A ASN* 1.3 65.9 + - - +
323A ALA* 3.2 8.0 + - - +
324A PHE* 3.1 23.0 + - - +
349A GLN* 5.7 0.7 - - - -
350A ILE* 4.3 8.3 - - + +
402A LEU* 4.4 2.2 - - + -
429A TYR 5.1 0.7 - - - +
432A GLY 4.2 5.4 - - - +
433A PHE* 4.0 38.6 - - + +
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Residues in contact with ASN 321 (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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68A PHE* 4.7 5.9 - - - -
72A MET* 4.2 8.9 - - + +
257A THR* 4.8 0.9 - - - +
258A ILE* 2.9 35.6 + - + +
259A ALA* 3.7 9.9 - - - +
317A ARG* 2.8 43.1 + - - +
318A TYR* 3.2 6.6 + - - +
320A ALA* 1.3 77.8 - - - +
322A THR* 1.3 61.2 + - - +
324A PHE* 3.4 2.9 + - - +
325A VAL* 3.3 25.8 + - - +
428A ASP* 4.5 7.1 + - - +
429A TYR 5.3 0.7 - - - +
431A ALA* 5.3 0.3 - - - +
432A GLY* 3.4 28.0 + - - -
433A PHE 4.5 0.3 + - - -
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Residues in contact with THR 322 (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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257A THR* 2.7 21.7 + - - -
287A TRP* 4.1 13.0 - - + -
288A LEU* 3.9 20.6 - - + +
291A TRP* 3.4 31.1 - - + -
318A TYR 3.0 12.7 + - - -
319A ALA 3.7 6.7 - - - -
321A ASN* 1.3 75.8 - - - +
323A ALA* 1.3 57.9 + - - +
324A PHE 3.3 0.2 + - - -
325A VAL* 3.3 2.1 + - - +
326A ALA* 2.8 27.9 + - - +
345A PHE* 3.6 22.4 - - + -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA 2.9 18.1 + - - +
320A ALA 3.2 5.8 + - - +
322A THR* 1.3 77.3 - - - +
324A PHE* 1.3 62.9 + - - +
326A ALA 3.4 0.2 + - - -
327A LEU* 3.1 22.0 + - - +
345A PHE* 4.1 4.7 - - - -
346A ALA* 3.3 43.2 - - + +
349A GLN* 4.4 6.1 - - + -
350A ILE* 3.9 19.3 - - + -
436A ALA* 4.8 0.2 - - - -
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Residues in contact with PHE 324 (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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72A MET* 3.9 19.3 - - + -
75A TRP* 3.5 38.1 - + + -
76A GLY* 3.8 18.6 - - - -
79A GLU* 4.2 1.6 - - + -
320A ALA 3.1 7.1 + - - +
321A ASN 3.7 6.5 - - - +
322A THR 3.2 0.4 - - - -
323A ALA* 1.3 76.9 - - - +
325A VAL* 1.3 67.8 + - + +
327A LEU* 3.1 13.4 + - - +
328A VAL* 3.1 31.0 + - + +
432A GLY* 3.6 18.2 - - - +
435A SER* 3.5 46.2 - - - -
436A ALA* 4.1 9.8 - - + +
439A MET* 4.1 14.1 - - + -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 5.1 0.9 - - + -
75A TRP* 4.1 26.2 - - + -
258A ILE* 3.9 22.7 - - + -
265A TYR 4.8 2.5 - - - +
266A GLY* 5.0 1.3 - - - -
269A VAL* 3.5 36.1 - - + -
287A TRP* 3.6 21.3 - - + -
288A LEU* 5.3 0.2 - - + -
321A ASN 3.3 13.2 + - - +
322A THR 3.3 3.9 + - - +
324A PHE* 1.3 79.5 - - + +
326A ALA* 1.3 58.1 + - - +
328A VAL* 3.1 7.8 + - - +
329A TYR* 2.9 27.5 + - - +
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Residues in contact with ALA 326 (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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288A LEU* 4.0 23.0 - - + +
322A THR 2.8 18.4 + - - +
323A ALA 3.6 5.4 - - - +
324A PHE 3.2 0.2 - - - -
325A VAL* 1.3 76.0 - - - +
327A LEU* 1.3 57.4 + - - +
329A TYR* 3.9 0.9 - - - +
330A ALA* 2.9 31.4 + - - +
342A TYR* 3.8 29.9 - - + +
345A PHE* 4.0 15.0 - - + -
346A ALA* 4.2 0.4 - - + -
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Residues in contact with LEU 327 (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* 3.1 18.5 + - + +
324A PHE* 3.1 8.2 + - - +
326A ALA* 1.3 76.5 - - - +
328A VAL* 1.3 64.1 + - - +
330A ALA* 3.7 9.9 + - - +
331A LYS* 3.7 17.2 + - - +
343A HIS* 3.7 34.8 - - + +
346A ALA* 3.5 19.7 - - + -
347A VAL* 4.7 0.7 - - + -
350A ILE* 5.7 0.7 - - + -
436A ALA* 4.1 19.5 - - + +
439A MET* 3.5 43.0 - - + +
440A LEU* 4.2 20.2 - - + -
443A GLU* 5.1 2.0 - - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 4.4 12.3 - - + -
79A GLU* 3.6 35.4 - - + +
269A VAL* 4.2 15.9 - - + -
270A LEU* 5.6 0.2 - - + -
273A LYS* 4.1 14.8 - - + -
324A PHE* 3.1 42.5 + - + +
325A VAL* 3.1 8.4 + - - +
327A LEU* 1.3 76.9 - - - +
329A TYR* 1.3 63.9 + - - +
331A LYS* 3.1 20.1 + - - +
332A VAL* 3.7 8.0 - - - +
439A MET* 4.5 6.5 - - - -
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Residues in contact with TYR 329 (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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269A VAL* 4.0 24.2 - - + +
272A ALA* 4.2 13.5 - - + -
281A ILE* 3.4 31.1 + - + +
284A ALA* 3.6 19.7 - - + -
285A ASN* 3.1 34.0 + - - -
288A LEU* 3.6 25.6 - - + -
325A VAL 2.9 15.3 + - - +
326A ALA 3.9 3.4 - - - +
328A VAL* 1.3 73.7 - - - +
330A ALA* 1.3 58.5 + - - +
331A LYS 2.8 10.8 + - - -
332A VAL* 2.9 39.6 + - + +
333A ILE* 3.2 24.9 + - + +
342A TYR* 3.6 16.8 - + - -
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Residues in contact with ALA 330 (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 ALA 2.9 19.7 + - - +
327A LEU* 3.8 8.1 - - - +
328A VAL 3.3 0.4 - - - -
329A TYR* 1.3 74.8 - - - +
331A LYS* 1.3 59.0 + - + +
332A VAL 3.5 0.2 - - - -
333A ILE* 4.1 10.0 - - - +
339A LYS* 3.2 54.9 - - + +
342A TYR* 4.4 4.2 - - + -
343A HIS* 4.0 21.1 - - + +
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Residues in contact with LYS 331 (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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79A GLU* 5.0 11.8 + - - +
273A LYS* 6.5 0.4 - - - -
327A LEU 3.7 14.6 - - - +
328A VAL* 3.1 10.4 + - - +
329A TYR 2.9 1.4 - - - -
330A ALA* 1.3 82.3 - - + +
332A VAL* 1.3 62.8 + - + +
333A ILE 4.4 2.4 - - - +
339A LYS* 4.7 7.1 + - - +
439A MET* 3.9 24.3 - - + +
442A GLU* 3.5 23.2 + - - -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 5.9 0.4 - - + -
272A ALA* 5.1 2.9 - - + +
273A LYS* 3.6 51.1 - - + +
281A ILE* 6.5 0.4 - - + -
328A VAL* 3.7 15.7 - - + +
329A TYR* 2.9 35.7 + - + +
331A LYS* 1.3 81.9 - - + +
333A ILE* 1.3 68.6 + - - +
334A ASP* 3.7 8.8 + - - +
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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