Contacts of the helix formed by residues 292 - 313 (chain H) in PDB entry 3DBL
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 VAL 292 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 4.0 18.6 - - + +
19G LEU* 3.5 19.5 - - + -
20G TRP* 4.0 20.4 - - + -
52G PRO* 6.5 0.2 - - + -
89H ASN* 4.8 2.9 - - - +
90H ARG* 4.0 7.4 - - - -
184H GLY 4.0 8.2 + - - +
185H PHE* 3.9 12.6 - - + -
291H ALA* 1.3 82.6 - - - +
293H ALA* 1.3 68.5 + - - +
294H SER* 3.6 19.3 - - - +
295H THR* 3.6 19.8 - - - +
296H ASN* 3.5 19.3 + - - +
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Residues in contact with ALA 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 5.9 0.2 + - - -
48G ASN* 3.4 29.2 - - - +
51G LEU* 4.1 20.0 - - + -
52G PRO* 4.8 3.4 - - + +
62H GLU* 4.5 3.9 - - - +
89H ASN 4.0 16.7 + - - +
90H ARG* 3.7 18.0 - - - +
292H VAL* 1.3 74.3 - - - +
294H SER* 1.3 59.0 + - - +
296H ASN* 3.2 5.1 + - - +
297H ALA* 2.9 27.5 + - - +
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Residues in contact with SER 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TRP* 6.1 0.3 - - - -
48G ASN* 3.6 18.0 + - - +
499G GLY* 3.6 21.3 - - - -
502G ALA* 4.8 0.9 - - - -
503G GLN* 3.5 31.6 - - - +
506G ILE* 5.8 1.7 - - - +
292H VAL* 3.6 13.7 - - - +
293H ALA* 1.3 75.8 - - - +
295H THR* 1.3 66.4 + - - +
297H ALA* 3.1 4.7 + - - +
298H VAL* 3.0 28.4 + - - +
326H ASP* 5.3 1.3 - - - -
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Residues in contact with THR 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H THR* 3.4 17.5 - - - +
184H GLY 2.9 27.4 + - - +
185H PHE* 3.5 24.4 + - - +
186H LYS 3.7 15.9 - - - +
187H GLY* 4.6 3.6 - - - +
292H VAL* 3.6 12.9 + - - +
293H ALA 3.5 0.8 - - - -
294H SER* 1.3 78.0 + - - +
296H ASN* 1.3 63.5 + - - +
298H VAL* 3.2 8.1 + - - +
299H ILE* 3.2 24.2 + - + +
324H PHE* 4.9 7.1 - - + -
326H ASP* 4.8 4.7 + - - -
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Residues in contact with ASN 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLY* 4.1 22.4 - - - +
59H LEU* 3.9 20.6 - - - +
62H GLU* 4.5 3.1 - - - +
90H ARG* 3.6 28.5 - - + +
182H THR* 3.3 32.5 + - - +
291H ALA* 4.9 1.2 - - - +
292H VAL 3.5 16.5 + - - +
293H ALA* 3.2 8.3 + - - +
295H THR* 1.3 79.1 - - - +
297H ALA* 1.3 62.5 + - - +
299H ILE 3.6 0.2 + - - -
300H ALA* 3.0 29.3 + - - +
176L GLY* 3.7 9.9 + - - +
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Residues in contact with ALA 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 6.0 0.4 - - - +
48G ASN* 3.9 22.2 - - - +
495G ALA* 3.9 11.0 - - + +
499G GLY* 4.1 6.5 - - - -
62H GLU* 3.5 32.2 + - - +
66H ASN* 4.8 0.2 + - - -
293H ALA 2.9 12.4 + - - +
294H SER 3.1 9.2 + - - +
296H ASN* 1.3 76.4 - - - +
298H VAL* 1.3 58.5 + - - +
300H ALA* 3.9 1.0 - - - +
301H ALA* 3.0 28.8 + - - +
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Residues in contact with VAL 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G PHE* 3.6 32.7 - - + +
499G GLY* 3.8 2.7 - - - -
500G ALA* 3.6 26.5 - - - +
294H SER 3.0 22.0 + - - +
295H THR* 3.5 8.3 - - - +
296H ASN 3.2 0.2 - - - -
297H ALA* 1.3 74.8 - - - +
299H ILE* 1.3 70.5 + - + +
301H ALA* 2.9 17.9 + - - +
302H VAL* 3.0 14.0 + - + +
322H LEU* 6.5 0.4 - - + -
324H PHE* 3.7 40.8 - - + -
326H ASP* 5.5 0.9 - - - +
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Residues in contact with ILE 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 3.8 20.6 - - + -
180H GLY* 3.8 22.9 - - - -
181H GLY 3.6 15.9 - - - +
182H THR* 4.5 3.8 - - - +
187H GLY* 3.5 12.6 - - - +
188H ASN* 3.4 32.1 - - - +
189H ALA* 3.9 7.2 - - + +
295H THR* 3.2 16.0 + - + +
298H VAL* 1.3 81.5 - - + +
300H ALA* 1.3 58.8 + - - +
302H VAL* 3.0 9.8 + - + +
303H CYS* 2.9 28.8 + - - -
322H LEU* 4.9 4.5 - - + -
324H PHE* 4.4 13.9 - - + -
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Residues in contact with ALA 300 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 3.9 23.8 - - + +
62H GLU* 3.6 26.5 - - + -
63H LEU* 4.0 9.8 - - + +
66H ASN* 3.6 2.1 + - - +
296H ASN 3.0 17.4 + - - +
299H ILE* 1.3 77.1 - - - +
301H ALA* 1.3 60.8 + - - +
303H CYS* 3.9 7.0 - - - +
304H ALA* 2.8 31.7 + - - +
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Residues in contact with ALA 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492G THR* 3.2 23.2 - - - +
495G ALA* 3.8 4.9 - - + -
496G PHE* 3.4 23.8 - - + +
522G TYR* 5.5 0.7 - - - -
66H ASN* 3.7 10.3 - - - +
297H ALA 3.0 14.9 + - - +
298H VAL 2.9 10.5 + - - +
300H ALA* 1.3 77.5 - - - +
302H VAL* 1.3 63.0 + - - +
304H ALA* 3.6 2.2 - - - +
305H THR* 3.0 28.1 + - - -
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Residues in contact with VAL 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G PHE* 3.7 25.8 - - + -
522G TYR* 4.0 8.1 - - - +
527G GLN* 3.6 25.3 + - + +
189H ALA* 3.5 23.6 - - + -
298H VAL* 3.0 16.3 + - + +
299H ILE* 3.0 10.9 + - + +
301H ALA* 1.3 74.4 - - - +
303H CYS* 1.3 68.1 + - - +
305H THR* 3.1 14.4 + - - -
306H GLU* 3.1 17.8 + - + +
318H LEU* 5.3 2.7 - - + -
322H LEU* 4.2 19.5 - - + -
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Residues in contact with CYS 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 5.4 1.3 - - - -
63H LEU* 4.0 15.0 - - + -
142H VAL* 4.4 1.8 - - + -
143H CYS 5.0 3.6 - - - -
178H ILE* 3.8 24.9 - - + +
179H ASP* 4.1 1.3 - - - -
180H GLY* 3.8 33.9 - - - -
189H ALA* 4.0 13.0 - - - -
299H ILE* 2.9 24.3 + - - +
300H ALA* 3.9 5.6 - - - +
302H VAL* 1.3 73.1 - - - +
304H ALA* 1.3 65.4 + - - +
306H GLU* 3.1 6.7 + - - +
307H VAL* 3.0 26.4 + - - +
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Residues in contact with ALA 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492G THR* 3.6 12.2 - - + +
63H LEU* 4.0 11.8 - - + +
66H ASN* 3.3 32.1 - - + +
67H LEU* 4.3 14.9 - - + +
70H SER* 5.4 0.7 + - - -
300H ALA 2.8 22.5 + - - +
301H ALA 3.6 1.8 - - - +
303H CYS* 1.3 74.1 - - - +
305H THR* 1.3 63.0 + - - +
307H VAL* 3.2 5.2 + - - +
308H PHE* 3.1 20.1 + - - +
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Residues in contact with THR 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G LEU* 4.8 7.0 - - + -
492G THR* 2.8 31.7 + - - +
493G ILE* 4.2 12.9 - - + +
522G TYR* 5.3 1.3 + - - -
524G GLY 3.9 10.8 - - - +
527G GLN* 3.6 22.0 - - - +
301H ALA 3.0 10.8 + - - -
302H VAL* 3.1 9.7 + - - -
304H ALA* 1.3 77.3 - - - +
306H GLU* 1.3 63.0 + - - +
308H PHE* 3.2 11.9 + - + +
309H LYS* 3.0 29.3 + - + +
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Residues in contact with GLU 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527G GLN* 2.9 25.0 + - + +
178H ILE* 3.8 14.6 - - + -
191H VAL* 4.0 17.8 - - + +
302H VAL* 3.1 17.7 + - + +
303H CYS* 3.1 11.2 + - - +
305H THR* 1.3 72.3 - - - +
307H VAL* 1.3 69.4 + - - +
309H LYS* 2.9 39.8 + - - +
310H ILE* 2.9 17.3 + - + +
317H PRO* 3.3 13.0 - - - +
318H LEU* 2.8 31.7 + - + +
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Residues in contact with VAL 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H VAL* 4.6 6.1 - - + -
67H LEU* 3.9 20.9 - - + -
72H PHE* 3.9 12.6 - - + -
140H ILE* 3.6 32.1 - - + +
142H VAL* 3.7 26.0 - - + -
178H ILE* 3.3 24.9 - - + +
303H CYS 3.0 15.6 + - - +
304H ALA 3.4 7.6 - - - +
306H GLU* 1.3 76.8 - - - +
308H PHE* 1.3 64.2 + - - +
310H ILE* 3.2 4.1 + - - +
311H ALA* 3.1 20.1 + - - +
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Residues in contact with PHE 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492G THR* 6.0 1.1 - - + +
20H VAL* 3.9 22.2 - - + -
23H PHE* 4.5 11.7 - + + -
24H LEU* 4.1 9.9 - - + -
45H LEU* 4.2 5.4 - - + -
70H SER* 3.6 33.9 - - - +
72H PHE* 3.7 24.0 - + + -
304H ALA 3.1 11.8 + - - +
305H THR* 3.2 15.5 - - + +
306H GLU 3.0 0.4 - - - -
307H VAL* 1.3 78.5 - - - +
309H LYS* 1.3 61.7 + - + +
311H ALA* 3.3 0.9 + - - -
312H THR* 2.6 64.8 + - + +
314H ALA* 4.1 14.4 - - + -
315H TYR* 5.9 1.3 - + - -
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Residues in contact with LYS 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G LEU* 5.7 1.8 - - - -
524G GLY 3.3 25.2 + - - -
525G MET* 3.7 11.1 + - - +
527G GLN* 3.8 2.6 - - - +
305H THR* 3.0 22.0 + - + +
306H GLU* 2.9 39.4 + - - +
308H PHE* 1.3 81.2 - - + +
310H ILE* 1.3 58.6 + - - +
312H THR* 3.8 4.9 - - - -
313H SER* 2.5 35.5 + - - +
314H ALA 4.6 1.6 - - - +
315H TYR* 3.4 46.8 - - + +
316H ILE 3.3 25.0 + - - +
317H PRO* 4.6 7.4 - - + +
318H LEU* 4.3 0.8 - - - +
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Residues in contact with ILE 310 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H ILE* 4.3 11.2 - - + -
176H PRO* 3.8 36.3 - - + -
178H ILE* 3.4 36.3 - - + -
191H VAL* 4.1 17.7 - - + -
193H LEU* 5.4 5.2 - - + -
306H GLU* 2.9 8.7 + - + +
307H VAL 3.2 6.3 + - - +
309H LYS* 1.3 75.0 - - - +
311H ALA* 1.3 59.1 + - - +
313H SER* 4.7 5.7 + - - -
317H PRO* 4.2 23.8 - - + -
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Residues in contact with ALA 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H LEU* 3.9 14.8 - - + +
49H CYS* 4.1 11.0 - - - -
72H PHE* 3.8 27.1 - - + -
140H ILE* 4.2 7.6 - - + -
307H VAL 3.1 14.3 + - - +
308H PHE 3.9 1.3 - - - +
310H ILE* 1.3 77.0 - - - +
312H THR* 1.3 61.4 + - - +
313H SER* 5.3 0.2 - - - -
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Residues in contact with THR 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H LEU* 3.4 32.4 - - + +
35H PHE* 3.5 12.3 - - - -
41H SER* 6.4 0.4 - - - -
45H LEU* 3.9 19.7 - - + -
308H PHE* 2.6 50.0 + - + +
311H ALA* 1.3 82.8 - - - +
313H SER* 1.3 73.6 + - - +
314H ALA* 3.4 9.5 + - - +
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Residues in contact with SER 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H THR* 3.7 1.0 + - - -
32H HIS* 3.7 26.2 - - - +
34H ASP* 4.3 7.1 + - - +
35H PHE* 2.8 42.6 - - - +
309H LYS 2.5 23.0 + - - -
310H ILE* 4.7 5.7 + - - -
311H ALA 3.8 0.5 - - - -
312H THR* 1.3 76.5 - - - +
314H ALA* 1.3 56.5 + - - +
315H TYR 3.3 10.1 - - - -
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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