Contacts of the helix formed by residues 315 - 332 (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 ALA 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET* 3.5 14.0 - - + +
308B ALA 4.5 2.8 - - - +
309B VAL* 4.5 7.0 - - + -
310B LEU 5.4 1.6 + - - +
311B ASP 3.5 22.9 - - - +
312B THR 4.3 2.1 + - - +
313B TRP 3.2 2.9 - - - -
314B GLY* 1.3 75.3 - - - +
316B LEU* 1.3 63.6 + - - +
318B TYR* 3.2 8.8 + - - +
319B ALA* 3.1 21.3 + - - +
404B GLY 3.5 6.8 + - - +
406B PRO 3.2 28.3 - - - +
407B GLY* 4.6 1.6 - - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET* 3.9 28.0 - - + -
315B ALA* 1.3 75.9 - - - +
317B ARG* 1.3 60.2 + - - +
319B ALA* 3.8 7.7 - - + +
320B ALA* 2.8 32.2 + - - +
349B GLN 5.3 2.9 - - - +
352B TYR* 4.2 15.5 - - + -
353B ALA* 4.3 13.5 - - + -
363B TYR* 3.5 40.2 - - + -
402B LEU* 4.2 14.9 - - + +
403B VAL 3.8 18.4 - - - +
404B GLY 3.1 11.7 + - - +
405B GLY* 3.8 11.4 - - - -
406B PRO* 4.5 0.7 - - + -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA* 4.7 1.5 - - - +
260B TRP* 3.7 20.8 - - - +
313B TRP* 3.1 31.3 + - - +
314B GLY* 2.9 18.8 + - - +
316B LEU* 1.3 77.6 - - - +
318B TYR* 1.3 86.0 + - - +
320B ALA* 3.3 2.8 + - - +
321B ASN* 2.8 52.4 + - - +
402B LEU* 4.3 10.0 - - - +
403B VAL 5.1 1.0 + - - -
428B ASP* 2.7 48.7 + - - +
429B TYR* 3.6 48.9 + - + +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TRP* 3.9 28.7 + + - -
257B THR* 3.5 23.7 - - + +
258B ILE 4.9 0.2 - - - -
259B ALA* 3.9 21.3 - - + +
260B TRP* 5.3 3.6 + - - -
291B TRP* 4.3 1.8 - - + -
310B LEU* 3.8 23.3 - - + -
311B ASP* 3.8 25.3 + - + -
313B TRP* 3.1 29.8 - - + +
314B GLY 2.9 12.9 + - - -
315B ALA* 3.2 8.7 + - - +
317B ARG* 1.3 101.9 + - - +
319B ALA* 1.3 63.4 + - - +
321B ASN* 3.2 4.1 + - - +
322B THR* 3.0 27.8 + - - -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 4.2 14.3 - - + -
307B MET* 5.4 1.6 - - + -
308B ALA 3.9 14.1 + - - +
315B ALA 3.1 13.4 + - - +
316B LEU* 3.4 15.9 + - + +
318B TYR* 1.3 75.3 - - - +
320B ALA* 1.3 57.9 + - - +
322B THR* 3.4 3.3 + - - -
323B ALA* 2.9 29.4 + - - +
345B PHE* 4.8 0.2 - - - -
349B GLN* 3.9 34.3 - - + +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU 2.8 19.3 + - - +
317B ARG* 3.6 7.0 - - - +
319B ALA* 1.3 75.8 - - - +
321B ASN* 1.3 65.4 + - - +
323B ALA* 3.2 8.3 + - - +
324B PHE* 3.0 22.7 + - - +
349B GLN* 5.7 0.7 - - - -
350B ILE* 4.2 8.5 - - + +
402B LEU* 4.4 2.0 - - + -
429B TYR 5.1 0.4 - - - +
432B GLY 4.2 4.9 - - - +
433B PHE* 4.0 38.4 - - + +
436B ALA* 4.7 0.2 - - - +
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.6 6.7 - - - -
72B MET* 4.2 8.5 - - + +
257B THR* 4.9 0.9 - - - +
258B ILE* 3.0 34.4 + - + +
259B ALA* 3.8 10.7 - - - +
317B ARG* 2.8 41.7 + - - +
318B TYR* 3.6 5.9 - - - +
320B ALA* 1.3 77.5 - - - +
322B THR* 1.3 62.3 + - - +
324B PHE* 3.3 3.6 + - - +
325B VAL* 3.3 26.2 + - - +
428B ASP* 4.5 6.6 + - - +
429B TYR 5.3 0.7 - - - +
431B ALA* 5.3 0.2 - - - +
432B GLY* 3.4 28.6 + - - -
433B PHE 4.5 0.7 + - - -
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B THR* 2.8 22.8 + - - -
287B TRP* 4.1 11.2 - - + -
288B LEU* 3.9 16.8 - - + +
291B TRP* 3.4 35.9 - - + -
318B TYR 3.0 12.6 + - - -
319B ALA 3.7 6.7 - - - -
321B ASN* 1.3 72.7 - - - +
323B ALA* 1.3 60.7 + - - +
325B VAL* 3.4 2.1 + - - +
326B ALA* 2.9 28.8 + - - +
345B PHE* 3.6 23.3 - - + -
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA 2.9 18.5 + - - +
320B ALA* 3.2 6.9 + - - +
322B THR* 1.3 77.3 - - - +
324B PHE* 1.3 62.7 + - - +
327B LEU* 3.1 21.7 + - - +
345B PHE* 4.1 4.9 - - + -
346B ALA* 3.3 44.6 - - + +
349B GLN* 4.4 5.2 - - + -
350B ILE* 3.9 18.2 - - + -
436B ALA* 4.8 0.2 - - - -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.9 19.7 - - + -
75B TRP* 3.6 39.5 - + + -
76B GLY* 3.8 17.7 - - - -
79B GLU* 4.2 1.6 - - + -
320B ALA 3.0 8.1 + - - +
321B ASN 3.7 7.0 - - - +
323B ALA* 1.3 76.8 - - - +
325B VAL* 1.3 68.5 + - + +
327B LEU* 3.0 13.6 + - - +
328B VAL* 3.1 30.6 + - + +
432B GLY* 3.6 18.6 - - - +
435B SER* 3.5 46.2 - - - -
436B ALA* 3.7 9.6 - - + +
439B MET* 4.1 14.6 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 5.1 0.4 - - + -
75B TRP* 4.1 25.1 - - + -
258B ILE* 3.9 23.1 - - + -
265B TYR 4.7 1.8 - - - +
266B GLY* 5.0 1.3 - - - -
269B VAL* 3.5 36.1 - - + -
287B TRP* 3.6 22.9 - - + -
288B LEU* 5.3 0.2 - - + -
321B ASN 3.3 15.0 + - - +
322B THR 4.0 1.8 - - - +
324B PHE* 1.3 78.6 - - + +
326B ALA* 1.3 57.0 + - - +
328B VAL* 3.1 8.7 + - - +
329B TYR* 2.9 27.5 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 3.9 23.9 - - + +
322B THR 2.9 17.7 + - - +
323B ALA 3.6 5.4 - - - +
325B VAL* 1.3 75.9 - - - +
327B LEU* 1.3 57.6 + - - +
329B TYR* 3.8 1.0 - - - +
330B ALA* 2.9 31.6 + - - +
342B TYR* 3.8 28.2 - - + +
345B PHE* 4.0 15.3 - - + -
346B ALA* 4.3 0.9 - - + -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA* 3.1 18.0 + - + +
324B PHE* 3.0 9.0 + - - +
326B ALA* 1.3 76.5 - - - +
328B VAL* 1.3 64.7 + - - +
330B ALA* 3.6 9.4 + - - +
331B LYS* 3.7 17.5 + - - +
343B HIS* 3.7 34.9 - - + +
346B ALA* 3.5 20.2 - - + -
347B VAL* 4.7 0.4 - - + -
350B ILE* 5.7 0.9 - - + -
436B ALA* 4.1 19.1 - - + +
439B MET* 3.7 40.6 - - + +
440B LEU* 4.2 20.4 - - + -
443B GLU* 5.0 2.2 - - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 4.4 13.0 - - + -
79B GLU* 3.7 34.1 - - + +
269B VAL* 4.2 16.4 - - + -
270B LEU* 5.6 0.2 - - + -
273B LYS* 4.1 14.3 - - + -
324B PHE* 3.1 41.8 + - + +
325B VAL* 3.1 8.8 + - - +
327B LEU* 1.3 76.6 - - - +
329B TYR* 1.3 64.1 + - - +
331B LYS* 3.1 20.5 + - - +
332B VAL* 3.7 7.6 - - + +
439B MET* 4.0 9.0 - - + -
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 4.0 23.5 - - + +
272B ALA* 4.3 12.8 - - + -
281B ILE* 3.3 31.0 + - + +
284B ALA* 3.5 20.0 - - + -
285B ASN* 3.0 35.0 + - - -
288B LEU* 3.5 25.4 - - + -
325B VAL 2.9 15.3 + - - +
326B ALA 3.9 3.4 - - - +
328B VAL* 1.3 72.8 - - - +
330B ALA* 1.3 57.0 + - - +
331B LYS 2.8 11.3 + - - -
332B VAL* 2.8 42.3 + - + +
333B ILE* 3.2 23.7 + - + +
342B TYR* 3.6 16.6 - + - -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA 2.9 19.2 + - - +
327B LEU* 3.8 8.5 - - - +
328B VAL 3.3 0.2 - - - -
329B TYR* 1.3 74.6 - - - +
331B LYS* 1.3 60.0 + - + +
332B VAL 3.5 0.2 - - - -
333B ILE* 4.1 9.6 - - - +
339B LYS* 3.2 55.0 - - + +
342B TYR* 4.4 4.7 - - + -
343B HIS* 4.1 20.6 - - + +
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 5.1 10.4 + - - +
80B SER* 6.0 0.2 - - - -
273B LYS* 6.5 0.4 - - - -
327B LEU 3.7 13.9 - - - +
328B VAL* 3.1 9.6 + - - +
329B TYR 2.8 1.2 + - - -
330B ALA* 1.3 82.5 - - + +
332B VAL* 1.3 63.5 + - + +
333B ILE 4.4 2.8 - - - +
339B LYS* 4.7 7.3 + - - +
439B MET* 4.4 22.6 - - + +
442B GLU* 3.5 23.2 + - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 5.8 0.2 - - + -
272B ALA* 5.1 2.9 - - + +
273B LYS* 3.6 51.8 - - + +
281B ILE* 6.4 0.7 - - + -
328B VAL* 3.7 15.0 - - + +
329B TYR* 2.8 36.2 + - + +
331B LYS* 1.3 79.8 - - + +
333B ILE* 1.3 67.9 + - - +
334B ASP* 3.7 9.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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