Contacts of the helix formed by residues 284 - 302 (chain B) in PDB entry 1H3F
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 GLY 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU 3.7 0.9 + - - +
281B LEU* 3.0 13.3 + - - -
282B LYS 3.3 1.0 + - - -
283B ALA* 1.3 80.8 - - - +
285B PRO* 1.3 76.3 - - - +
287B PRO* 3.2 8.5 - - - +
288B ALA* 3.0 24.7 + - - +
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Residues in contact with PRO 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP* 3.4 33.2 - - - +
262B LEU* 4.5 6.5 - - + -
281B LEU 5.3 0.4 - - - +
284B GLY* 1.3 79.5 - - - +
286B VAL* 1.3 65.5 + - + +
287B PRO* 4.8 0.4 - - + -
288B ALA* 3.2 6.8 + - + +
289B HIS* 2.8 37.5 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 4.6 8.3 - - + -
285B PRO* 1.3 78.3 - - + +
287B PRO* 1.3 75.3 - - + +
289B HIS* 3.1 9.7 + - - +
290B ARG* 3.0 50.6 + - + +
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Residues in contact with PRO 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.3 3.8 - - + -
283B ALA* 3.4 29.8 - - + +
284B GLY* 3.2 17.3 - - - +
285B PRO* 4.8 0.4 - - + -
286B VAL* 1.3 95.5 - - + +
288B ALA* 1.3 62.9 + - - +
290B ARG* 3.1 21.5 + - + +
291B VAL* 3.3 16.0 + - - +
324B PHE 3.8 20.4 - - - +
325B GLY* 4.3 1.5 - - - -
326B ARG* 5.3 13.7 - - + +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.0 20.0 - - + -
266B PHE* 3.5 24.3 - - + -
280B LEU* 3.6 25.0 - - + +
281B LEU* 4.4 6.7 - - + -
284B GLY 3.0 18.8 + - - +
285B PRO 3.4 4.5 - - - +
287B PRO* 1.3 78.5 - - - +
289B HIS* 1.3 60.6 + - - +
290B ARG 3.3 0.3 + - - -
291B VAL* 3.3 1.9 + - - +
292B LEU* 3.1 17.8 + - - +
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Residues in contact with HIS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU 3.3 19.6 - - - +
255B MET* 3.1 41.4 + - + +
257B VAL* 2.7 24.9 + - + -
259B ASP* 3.3 25.6 - - - -
262B LEU* 3.7 28.9 - - + +
285B PRO* 2.8 28.6 + - + -
286B VAL* 3.5 10.0 + - - +
288B ALA* 1.3 76.2 - - - +
290B ARG* 1.3 57.1 + - - +
292B LEU* 3.8 6.0 - - + +
293B ALA* 2.9 32.2 + - - +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 5.0 1.5 - - - -
255B MET* 3.9 21.8 - - + +
286B VAL* 3.0 36.5 + - - +
287B PRO* 3.1 10.3 + - - +
289B HIS* 1.3 75.5 - - - +
291B VAL* 1.3 66.0 + - - +
293B ALA* 3.9 1.5 - - - +
294B ARG* 2.9 33.9 + - - +
325B GLY* 3.6 32.5 - - - +
326B ARG* 5.5 0.7 - - - +
328B LYS* 4.0 9.0 - - - +
339B GLU* 2.8 38.5 + - - +
342B TYR* 5.5 0.6 - - - -
343B ASP* 2.7 39.1 + - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 5.0 0.4 - - + -
272B LEU* 4.8 0.2 - - + -
280B LEU* 3.5 42.8 - - + -
287B PRO 3.3 7.0 + - - +
288B ALA 3.8 5.2 - - - +
290B ARG* 1.3 75.5 - - - +
292B LEU* 1.3 57.6 + - - +
294B ARG* 3.7 2.5 - - - +
295B LEU* 2.9 46.8 + - + +
314B TYR* 4.0 28.9 - - + +
321B TRP* 4.2 12.6 - - + -
324B PHE* 4.5 1.1 - - - -
325B GLY* 3.9 21.8 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 4.4 22.4 - - + +
257B VAL* 4.6 2.2 - - + -
262B LEU* 4.1 22.4 - - + -
265B TYR* 4.2 34.1 - - + +
266B PHE* 3.7 28.2 - - + -
270B THR* 4.4 9.4 - - + -
288B ALA 3.1 16.2 + - - +
289B HIS* 3.8 3.6 - - - +
291B VAL* 1.3 77.6 - - - +
293B ALA* 1.3 62.3 + - - +
295B LEU* 3.4 4.6 + - - +
296B LEU* 3.0 55.8 + - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.6 31.4 - - + +
254B LEU* 3.7 28.3 - - + -
255B MET* 3.9 8.5 - - - -
289B HIS 2.9 19.7 + - - +
290B ARG 3.9 0.4 - - - +
292B LEU* 1.3 76.6 - - - +
294B ARG* 1.3 57.8 + - - +
297B THR* 2.4 36.6 + - - -
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.9 7.4 - - + -
290B ARG* 2.9 24.6 + - - +
291B VAL 3.7 3.6 - - - +
293B ALA* 1.3 75.0 - - - +
295B LEU* 1.3 65.2 + - - +
297B THR* 4.0 0.2 - - - -
298B ALA* 3.0 28.6 + - - +
314B TYR* 2.9 34.0 + - + -
317B LEU* 4.4 2.5 - - - +
319B TYR* 3.3 40.4 - - + +
325B GLY* 2.7 26.7 + - - -
327B ASP* 3.0 18.6 + - - -
328B LYS* 2.7 20.8 - - - +
335B VAL* 3.8 13.3 - - + +
339B GLU* 2.6 41.5 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 5.2 0.7 - - + -
270B THR* 4.3 14.1 - - + -
272B LEU* 3.9 26.7 - - + -
291B VAL* 2.9 36.1 + - + +
292B LEU* 3.4 5.8 + - - +
294B ARG* 1.3 77.8 - - - +
296B LEU* 1.3 61.1 + - + +
299B ALA* 3.1 29.2 + - - +
309B ILE* 3.9 22.4 - - + +
310B ASP 3.9 6.5 - - - +
313B PHE* 3.7 22.6 - - + -
314B TYR* 3.9 33.8 - - + -
317B LEU* 4.9 2.0 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.2 7.4 - - + -
250B MET* 4.3 3.4 - - - -
254B LEU* 3.6 25.1 - - + -
269B LEU* 3.6 48.9 - - + +
270B THR* 4.3 8.1 - - + -
292B LEU* 3.0 38.4 + - + +
295B LEU* 1.3 77.9 - - - +
297B THR* 1.3 68.7 + - - +
299B ALA* 4.2 1.8 - - - -
300B TYR* 3.0 50.5 + - + +
309B ILE* 4.4 8.3 - - + -
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Residues in contact with THR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PRO* 3.6 38.6 - - + +
250B MET* 4.0 10.3 - - + +
251B PHE* 3.4 32.9 + - + -
254B LEU* 3.9 4.1 - - - +
293B ALA 2.4 25.8 + - - -
294B ARG* 4.0 2.0 - - - -
296B LEU* 1.3 76.6 - - - +
298B ALA* 1.3 64.0 + - - +
300B TYR* 3.8 1.2 - - - +
301B ALA* 3.1 25.1 + - + +
335B VAL* 4.3 17.9 - - + -
338B ALA* 5.1 1.1 - - + -
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG 3.0 18.4 + - - +
295B LEU 4.0 1.1 - - - +
297B THR* 1.3 77.7 - - - +
299B ALA* 1.3 65.1 + - - +
301B ALA* 2.9 17.9 + - - +
302B LEU* 3.4 17.1 + - + +
313B PHE* 4.3 2.2 - - + -
317B LEU* 3.8 33.7 - - + -
332B PRO* 4.9 1.3 - - + -
335B VAL* 3.8 18.6 - - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU 3.1 18.6 + - - +
296B LEU* 3.8 5.4 - - - +
298B ALA* 1.3 81.4 - - - +
300B TYR* 1.3 62.0 + - + +
301B ALA 3.4 0.3 + - - -
302B LEU* 3.5 21.9 + - - +
305B ILE* 3.5 22.4 + - + +
306B PRO* 4.5 3.1 - - + -
309B ILE* 4.0 25.6 - - + -
313B PHE* 4.0 17.6 - - + -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.0 19.5 - - + -
56B ALA* 3.5 21.2 - - + +
60B ARG* 4.2 15.2 - - - -
114B LYS* 3.0 38.5 + - + +
115B ILE* 3.8 20.4 - - + +
243B LEU* 3.9 31.5 - - + +
245B GLU 5.7 0.9 - - - +
250B MET* 4.0 23.6 - - + -
269B LEU* 5.4 2.6 + - + +
296B LEU* 3.0 47.9 + - + +
297B THR 3.8 0.9 - - - -
299B ALA* 1.3 74.0 - - + +
301B ALA* 1.3 60.0 + - - +
302B LEU 3.2 1.3 - - - -
305B ILE* 3.8 23.8 - - + +
309B ILE* 4.9 2.0 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 5.0 0.4 - - - -
247B PRO* 4.0 26.7 - - + -
297B THR* 3.1 18.2 + - + +
298B ALA* 2.9 9.7 + - - +
300B TYR* 1.3 77.3 - - - +
302B LEU* 1.3 65.3 + - + +
303B PRO* 4.6 1.2 - - - +
334B GLU* 4.5 15.7 - - + +
335B VAL* 6.1 1.3 - - + -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 3.3 18.5 + - - +
298B ALA 3.5 12.6 - - - +
299B ALA* 3.5 16.4 - - - +
300B TYR 3.2 1.6 - - - +
301B ALA* 1.3 84.0 - - + +
303B PRO* 1.3 77.1 - - + +
304B GLN* 3.3 19.3 + - - +
306B PRO* 4.3 16.4 - - + -
313B PHE* 4.4 13.9 - - + -
317B LEU* 6.3 0.4 - - + -
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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