Contacts of the helix formed by residues 295 - 315 (chain A) in PDB entry 2A3K
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 ILE 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 4.2 22.0 - - + -
128A ILE* 4.0 29.6 - - + -
291A CYS* 4.0 0.4 - - - -
293A ALA* 4.3 7.2 - - + -
294A GLY* 1.3 83.6 - - - +
296A GLY* 1.3 76.7 + - - +
298A THR* 4.0 1.4 - - - -
299A GLY 3.0 10.9 + - - -
330A ARG* 3.7 16.4 - - + +
331A GLY 3.4 17.9 - - - +
332A GLY 3.6 24.0 - - - +
333A MET* 3.2 8.8 - - - +
334A ILE 2.8 22.1 + - - -
335A GLN* 5.3 11.7 - - + +
501A PO4 3.3 9.8 + - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 1.3 80.0 - - - +
297A ARG* 1.3 62.6 + - - +
299A GLY* 3.5 0.2 - - - -
300A CYS* 3.0 21.8 + - - -
334A ILE 3.8 1.9 + - - -
335A GLN* 3.8 31.0 - - - -
339A GLN* 4.0 8.3 - - - -
501A PO4 2.8 22.4 + - - -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.4 28.4 + - + +
195A THR* 4.1 0.6 - - - +
255A TRP* 3.0 64.9 + - + +
256A PRO 3.9 4.9 - - - +
257A ASP* 3.3 23.4 + - - +
258A HIS 5.2 0.7 - - - +
291A CYS* 3.9 11.7 - - + +
292A SER* 3.7 10.1 - - - +
296A GLY* 1.3 71.5 - - - +
298A THR* 1.3 57.5 - - - +
300A CYS* 3.0 9.3 + - - +
301A PHE 2.9 26.7 + - - -
339A GLN* 4.5 7.2 - - - +
501A PO4 2.7 40.4 + - - +
502A PO4 2.7 43.4 + - - -
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 3.5 32.3 - - + -
194A LEU* 3.7 9.4 - - - +
289A VAL* 3.8 20.0 - - + +
290A HIS* 3.5 7.1 + - - -
291A CYS* 2.9 34.9 + - - -
294A GLY* 3.5 19.3 - - - +
297A ARG* 1.3 76.8 - - - +
299A GLY* 1.3 61.8 + - - +
301A PHE* 3.6 1.4 + - - +
302A ILE* 3.3 29.6 + - + +
333A MET* 4.3 1.8 - - + -
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE 3.0 23.4 + - - -
296A GLY 3.1 0.9 + - - -
298A THR* 1.3 73.8 - - - +
300A CYS* 1.3 59.8 + - - +
302A ILE 3.6 0.3 + - - -
303A ALA* 3.0 31.2 + - - +
326A LEU* 3.8 4.4 - - - +
333A MET* 3.8 18.6 - - - +
334A ILE* 3.6 16.6 - - - +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TRP* 3.4 28.9 - - + -
260A THR* 5.3 0.7 - - - -
296A GLY 3.0 18.5 + - - -
297A ARG 3.0 2.8 + - - +
299A GLY* 1.3 74.6 - - - +
301A PHE* 1.3 58.9 + - - +
303A ALA* 3.5 1.4 + - - +
304A THR* 2.6 35.0 + - - +
334A ILE* 4.2 17.0 - - - -
339A GLN* 3.7 45.1 - - - +
342A PHE* 6.2 2.0 - - + -
343A LEU* 4.5 5.0 - - + +
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Residues in contact with PHE 301 (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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165A TYR* 5.0 5.2 - + - -
192A VAL* 4.2 9.6 - - + -
194A LEU* 3.8 19.1 - - + -
255A TRP* 4.2 7.1 - - + -
267A LEU* 4.3 10.1 - - + -
270A LEU* 3.9 31.2 - - + -
271A VAL* 3.8 19.7 - - + -
274A VAL* 3.6 31.6 - - + -
287A ILE* 5.4 0.4 - - + -
289A VAL* 3.9 33.9 - - + -
297A ARG 2.9 14.7 + - - +
298A THR 4.0 2.7 - - - +
300A CYS* 1.3 75.2 - - - +
302A ILE* 1.3 70.5 + - + +
304A THR* 3.0 16.9 + - - -
305A ARG* 3.0 26.4 + - + -
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 4.6 2.0 - - + -
165A TYR* 3.5 55.0 - - + -
167A ALA* 4.5 5.4 - - + -
289A VAL* 4.2 9.0 - - + -
298A THR* 3.3 35.4 + - + +
299A GLY 4.2 2.5 - - - +
301A PHE* 1.3 90.1 - - + +
303A ALA* 1.3 61.9 + - - +
305A ARG* 3.1 14.1 + - - +
306A ILE* 3.1 17.8 + - + +
326A LEU* 3.7 22.9 - - + -
333A MET* 4.0 12.3 - - + -
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Residues in contact with ALA 303 (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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299A GLY 3.0 19.2 + - - +
300A CYS 4.0 1.3 - - - +
302A ILE* 1.3 77.7 - - - +
304A THR* 1.3 56.0 + - - +
307A GLY* 3.0 25.6 + - - -
322A ILE* 3.6 31.9 - - + +
323A VAL* 4.9 0.7 - - + -
326A LEU* 3.9 5.3 - - + +
334A ILE* 3.8 8.7 - - + -
343A LEU* 3.7 31.2 - - + +
347A LEU* 4.7 0.3 - - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.3 13.7 - - + +
268A LEU* 4.3 1.8 - - + -
271A VAL* 4.1 18.6 - - + -
300A CYS* 2.6 20.8 + - - +
301A PHE* 3.0 12.4 + - - -
303A ALA* 1.3 75.2 - - - +
305A ARG* 1.3 65.7 + - - +
308A CYS* 3.0 32.9 + - - -
343A LEU* 3.6 16.1 - - - +
346A THR* 3.6 28.3 - - + +
347A LEU* 3.7 5.5 - - + +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.9 12.1 - - - +
165A TYR* 3.0 33.2 + - + +
271A VAL* 3.9 28.4 - - + +
274A VAL* 4.3 16.3 + - + +
275A GLU* 4.1 22.0 - - - +
287A ILE* 3.7 24.0 - - - +
301A PHE* 3.0 31.8 + - + +
302A ILE* 3.1 6.5 + - - +
304A THR* 1.3 74.4 - - - +
306A ILE* 1.3 52.6 + - - +
308A CYS* 2.9 6.6 + - - +
309A GLN* 2.8 64.7 + - - +
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Residues in contact with ILE 306 (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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156A ARG 4.0 16.8 - - - +
157A GLY* 4.1 10.3 - - - +
158A TYR* 4.2 21.1 - - - +
159A ASP 5.4 0.7 - - - +
165A TYR* 4.1 12.6 - - - +
302A ILE* 3.1 31.7 + - + +
303A ALA 4.2 2.5 - - - +
305A ARG* 1.3 73.8 - - - +
307A GLY* 1.3 51.1 + - - +
309A GLN* 3.1 15.4 + - - +
310A GLN* 2.8 44.1 + - + +
322A ILE* 3.7 29.4 - - + -
325A GLN* 4.4 8.3 - - - +
326A LEU* 4.5 8.5 - - + -
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Residues in contact with GLY 307 (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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303A ALA 3.0 19.2 + - - -
305A ARG 3.2 0.2 - - - -
306A ILE* 1.3 75.3 - - - +
308A CYS* 1.3 57.2 + - - +
310A GLN* 3.3 3.1 + - - +
311A LEU* 3.0 32.7 + - - +
317A VAL* 3.6 21.5 - - - +
322A ILE* 3.8 5.1 - - - +
347A LEU* 3.6 15.3 - - - -
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Residues in contact with CYS 308 (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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268A LEU* 4.0 14.4 - - - -
271A VAL* 4.7 11.4 - - + -
304A THR* 3.0 23.2 + - - -
305A ARG* 2.9 10.3 + - - +
307A GLY* 1.3 71.9 - - - +
309A GLN* 1.3 67.9 + - + +
311A LEU 3.2 0.9 + - - -
312A LYS* 2.9 23.2 + - - +
347A LEU* 3.7 10.3 - - - -
350A TYR* 3.2 60.4 - - + +
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Residues in contact with GLN 309 (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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158A TYR* 3.4 41.2 + - + +
164A VAL* 5.9 0.8 - - - +
165A TYR* 4.1 5.9 + - - -
305A ARG* 2.8 56.4 + - - +
306A ILE* 3.3 20.3 + - - +
308A CYS* 1.3 72.7 - - + +
310A GLN* 1.3 61.3 + - - +
312A LYS* 3.9 5.4 - - - +
313A ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 310 (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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158A TYR* 3.7 23.2 - - + -
159A ASP 5.7 1.8 - - - +
306A ILE* 2.8 25.8 + - - +
307A GLY 3.5 7.6 - - - +
308A CYS 3.2 0.2 - - - -
309A GLN* 1.3 72.5 - - - +
311A LEU* 1.3 57.4 + - - +
313A ALA 3.3 0.7 + - - -
314A ARG* 2.9 53.8 + - - +
315A GLY 3.6 0.3 + - - -
316A GLU 3.3 16.1 - - - +
317A VAL* 3.4 5.0 - - + +
318A ASP* 2.8 36.1 + - - +
322A ILE* 3.5 29.0 - - - +
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Residues in contact with LEU 311 (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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84A ARG* 4.2 21.4 - - + -
87A LEU* 3.8 17.5 - - + -
307A GLY 3.0 18.9 + - - +
308A CYS 3.2 3.1 + - - +
310A GLN* 1.3 77.2 - - - +
312A LYS* 1.3 62.8 + - - +
315A GLY* 3.0 25.8 + - - +
316A GLU* 3.7 26.7 - - - +
317A VAL* 4.0 11.0 - - + +
347A LEU* 3.4 34.8 - - + +
350A TYR* 4.1 17.9 - - + -
351A ALA* 4.2 5.8 - - + -
354A LEU* 4.2 12.8 - - + +
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Residues in contact with LYS 312 (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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308A CYS 2.9 17.6 + - - +
309A GLN* 3.9 4.7 - - - +
311A LEU* 1.3 79.1 - - - +
313A ALA* 1.3 62.6 + - - +
315A GLY 4.8 0.2 + - - -
350A TYR* 3.8 20.1 - - - +
354A LEU* 4.3 18.2 - - + -
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Residues in contact with ALA 313 (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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158A TYR* 3.2 30.5 - - + +
309A GLN 3.0 15.0 + - - +
312A LYS* 1.3 80.5 - - - +
314A ARG* 1.3 61.9 + - + +
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Residues in contact with ARG 314 (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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158A TYR* 3.1 34.8 + - - +
159A ASP* 3.3 24.6 + - - +
310A GLN* 2.9 40.4 + - - +
313A ALA* 1.3 78.4 - - + +
315A GLY* 1.3 64.4 + - - +
316A GLU* 3.2 48.0 + - + +
318A ASP* 5.8 2.2 - - - +
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Residues in contact with GLY 315 (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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83A THR* 4.1 1.9 - - - +
84A ARG* 3.1 38.8 + - - +
310A GLN 3.6 0.6 + - - -
311A LEU* 3.0 23.6 + - - -
312A LYS 4.8 0.2 + - - -
313A ALA 3.8 0.4 - - - -
314A ARG* 1.3 77.9 - - - +
316A GLU* 1.3 58.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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