Contacts of the helix formed by residues 284 - 302 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU 3.4 1.4 + - - +
281A LEU* 2.6 22.2 + - - -
282A LYS 3.2 1.5 - - - -
283A ALA* 1.3 74.5 - - - +
285A PRO* 1.3 76.0 - - - +
286A VAL* 5.5 0.7 - - - -
287A PRO* 3.1 14.6 - - - +
288A ALA* 3.1 18.2 + - - +
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Residues in contact with PRO 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 3.7 31.6 - - + +
262A LEU* 4.7 5.4 - - + -
281A LEU 5.0 0.9 - - - +
284A GLY* 1.3 80.6 - - - +
286A VAL* 1.3 69.2 + - + +
287A PRO* 5.0 0.2 - - + -
288A ALA* 3.4 5.5 + - + +
289A HIS* 2.9 34.0 + - + -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A MET* 4.6 7.3 - - + +
284A GLY* 5.0 0.7 - - - -
285A PRO* 1.3 80.3 - - + +
287A PRO* 1.3 78.2 - - + +
289A HIS* 3.2 8.3 + - + +
290A ARG* 3.1 32.8 + - - +
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Residues in contact with PRO 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 5.1 2.5 - - + -
283A ALA* 3.7 30.5 - - + +
284A GLY* 3.1 18.2 - - - +
286A VAL* 1.3 102.6 - - + +
288A ALA* 1.3 60.9 + - - +
290A ARG* 3.3 7.8 + - + +
291A VAL* 3.1 29.2 + - - +
324A PHE* 3.4 26.8 - - + +
325A GLY* 5.1 0.7 - - - -
326A ARG* 6.5 0.4 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.8 20.9 - - + -
266A PHE* 3.5 20.3 - - + -
280A LEU* 4.1 23.9 + - + +
281A LEU* 4.4 5.6 - - + -
284A GLY 3.1 16.2 + - - +
285A PRO* 3.7 4.5 - - + +
287A PRO* 1.3 79.2 - - - +
289A HIS* 1.3 62.7 + - - +
291A VAL* 3.5 0.5 + - - +
292A LEU* 3.1 24.1 + - - +
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 3.2 17.6 + - - +
255A MET* 3.3 34.9 + - + -
257A VAL* 2.7 33.5 + - - -
259A ASP* 3.0 23.9 + - - -
262A LEU* 3.8 23.0 - - + +
285A PRO* 2.9 34.0 + - + +
286A VAL* 3.2 7.2 + - + +
288A ALA* 1.3 75.2 - - - +
290A ARG* 1.3 55.6 + - - +
292A LEU* 3.2 6.3 + - - +
293A ALA* 2.7 37.2 + - - +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 4.5 1.9 - - + -
255A MET* 3.6 27.0 - - + +
286A VAL* 3.1 24.7 + - - +
287A PRO* 3.8 5.6 - - - +
289A HIS* 1.3 77.6 - - - +
291A VAL* 1.3 56.3 + - - +
293A ALA* 3.7 1.2 - - - +
294A ARG* 2.8 45.3 + - - +
325A GLY* 3.7 26.9 - - - -
328A LYS* 3.5 21.5 - - - +
339A GLU* 2.9 33.9 + - - +
342A TYR* 4.3 9.7 - - - -
343A ASP* 2.9 28.7 + - - -
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.7 0.2 - - + -
280A LEU* 3.7 40.2 - - + -
287A PRO 3.1 17.6 + - - +
288A ALA 4.0 3.6 - - - +
290A ARG* 1.3 76.1 - - - +
292A LEU* 1.3 58.9 + - - +
294A ARG* 3.4 4.7 + - - +
295A LEU* 2.9 45.5 + - + +
314A TYR* 3.8 33.2 - - + +
321A TRP* 4.8 7.6 - - + -
324A PHE* 4.7 2.0 - - - -
325A GLY* 4.4 13.9 - - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 4.5 22.0 - - + +
257A VAL* 4.9 2.7 - - + -
262A LEU* 3.9 24.5 - - + -
265A TYR* 4.3 32.8 - - + -
266A PHE* 3.7 30.0 - - + -
270A THR* 4.4 7.9 - - + -
288A ALA 3.1 18.1 + - - +
289A HIS* 3.6 2.9 - - - +
291A VAL* 1.3 77.1 - - - +
293A ALA* 1.3 62.8 + - - +
295A LEU* 3.8 2.8 - - - +
296A LEU* 3.0 55.0 + - + +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.6 33.2 - - + +
254A LEU* 3.7 25.3 - - + +
255A MET* 3.9 9.9 - - - -
289A HIS 2.7 20.8 + - - +
290A ARG 3.8 0.9 - - - +
292A LEU* 1.3 75.1 - - - +
294A ARG* 1.3 56.1 + - - +
297A THR* 2.7 36.8 + - - -
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 4.0 7.0 - - + -
290A ARG* 2.8 28.3 + - - +
291A VAL 3.8 2.9 - - - +
293A ALA* 1.3 75.4 - - - +
295A LEU* 1.3 65.9 + - - +
298A ALA* 3.0 28.9 + - - +
314A TYR* 3.0 34.3 + - + -
317A LEU* 4.3 2.8 - - - +
319A TYR* 3.5 36.6 - - + +
325A GLY* 2.9 32.4 + - - -
327A ASP* 3.1 19.8 + - - -
328A LYS* 3.0 21.2 - - - +
335A VAL* 4.2 8.0 - - + +
339A GLU* 2.9 40.1 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.7 3.4 - - + -
270A THR* 4.3 15.7 - - + -
272A LEU* 4.1 31.2 - - + -
291A VAL* 2.9 29.0 + - + +
292A LEU* 3.8 2.9 - - - +
294A ARG* 1.3 77.8 - - - +
296A LEU* 1.3 62.9 + - + +
298A ALA* 4.8 0.4 - - - -
299A ALA* 3.0 29.1 + - - +
309A ILE* 4.1 14.0 - - + +
310A ASP 3.9 7.4 - - - +
313A PHE* 3.7 29.4 - - + -
314A TYR* 3.7 36.1 - - + -
317A LEU* 4.9 1.6 - - + -
321A TRP* 6.1 0.4 - - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.3 7.6 - - + -
250A MET* 3.7 4.3 - - - +
254A LEU* 3.6 24.9 - - + -
269A LEU* 3.7 50.0 - - + +
270A THR* 4.3 8.1 - - + -
292A LEU* 3.0 37.1 + - + +
295A LEU* 1.3 77.7 - - + +
297A THR* 1.3 65.2 + - - +
299A ALA* 4.4 1.6 - - - -
300A TYR* 3.0 48.1 + - + +
309A ILE* 4.3 9.2 - - + -
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Residues in contact with THR 297 (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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247A PRO* 3.6 39.2 - - + +
250A MET* 3.8 10.7 - - + +
251A PHE* 3.4 35.0 + - + -
254A LEU* 3.9 4.3 - - - +
293A ALA 2.7 29.7 + - - -
294A ARG 4.3 0.9 - - - -
296A LEU* 1.3 73.7 - - - +
298A ALA* 1.3 61.8 + - - +
300A TYR 3.9 0.7 - - - -
301A ALA* 3.0 27.3 + - + +
335A VAL* 4.5 11.2 - - + -
338A ALA* 4.5 4.5 - - + -
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Residues in contact with ALA 298 (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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294A ARG 3.0 20.2 + - - +
295A LEU 3.9 1.3 - - - +
297A THR* 1.3 75.0 - - - +
299A ALA* 1.3 67.4 + - - +
301A ALA* 3.3 12.5 + - - +
302A LEU* 3.3 18.1 + - - +
313A PHE* 4.2 2.0 - - + -
317A LEU* 3.6 35.2 - - + -
332A PRO* 4.9 0.9 - - + -
335A VAL* 3.6 23.0 - - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU 3.0 19.6 + - - +
296A LEU* 3.9 4.0 - - - +
298A ALA* 1.3 79.8 - - - +
300A TYR* 1.3 62.7 + - + +
302A LEU* 3.4 21.9 + - - +
305A ILE* 3.5 25.5 - - + +
306A PRO* 4.5 0.4 - - + -
309A ILE* 3.9 27.4 - - + -
313A PHE* 4.0 16.5 - - + -
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Residues in contact with TYR 300 (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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53A LEU* 3.8 22.9 - - + -
56A ALA* 3.5 20.1 - - + +
60A ARG* 3.7 18.9 - - - -
114A LYS* 2.9 40.2 + - + +
115A ILE* 3.8 22.4 - - + +
243A LEU* 3.8 27.6 - - + +
250A MET* 3.8 24.5 - - + -
269A LEU* 5.3 1.3 + - + +
296A LEU* 3.0 43.0 + - + +
297A THR 3.9 0.9 - - - -
299A ALA* 1.3 77.7 - - + +
301A ALA* 1.3 59.7 + - - +
302A LEU 3.2 1.3 - - - -
305A ILE* 3.7 22.4 - - + +
309A ILE* 4.6 1.9 - - + +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 4.9 1.0 + - - -
247A PRO* 4.0 23.8 - - + -
297A THR* 3.0 20.6 + - + +
298A ALA* 3.3 7.6 + - - +
300A TYR* 1.3 77.5 - - - +
302A LEU* 1.3 65.7 + - + +
303A PRO* 4.6 0.9 - - - +
334A GLU* 3.7 32.1 - - + +
335A VAL* 5.5 1.6 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 3.2 20.6 + - - +
298A ALA 3.3 16.4 - - - +
299A ALA* 3.5 17.5 - - - +
300A TYR 3.2 1.6 - - - +
301A ALA* 1.3 82.0 - - + +
303A PRO* 1.3 79.7 - - + +
304A GLN* 3.3 19.1 + - - +
306A PRO* 4.4 11.7 - - + -
313A PHE* 4.5 13.0 - - + -
317A LEU* 6.0 2.0 - - + -
334A GLU* 6.1 0.7 - - - +
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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