Contacts of the helix formed by residues 292 - 311 (chain A) in PDB entry 6UZA
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 ASP 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A SER* 4.0 2.2 - - - -
291A GLU* 1.3 78.7 - - + +
293A PRO* 1.3 62.7 - - - +
294A VAL* 3.4 5.7 + - - +
295A MET* 3.7 16.7 - - + +
296A THR* 3.1 24.9 + - - -
365A ARG* 3.1 24.8 + - - -
855A TYR* 2.9 30.7 + - + -
859A MET* 3.9 12.6 - - - +
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Residues in contact with PRO 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.3 24.8 - - - +
287A SER* 4.9 0.9 - - - -
290A SER* 3.6 10.8 - - - +
291A GLU 3.5 10.8 - - - +
292A ASP* 1.3 84.2 - - - +
294A VAL* 1.3 60.2 + - - +
295A MET 3.4 0.2 - - - -
296A THR* 3.9 3.0 - - - -
297A ALA* 2.9 31.2 + - - +
328A PHE* 3.7 23.6 - - + -
332A LEU* 4.5 3.6 - - + -
859A MET* 3.8 20.0 - - + -
863A ILE* 3.8 26.9 - - + -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 3.3 3.2 - - - +
293A PRO* 1.3 75.0 - - - +
295A MET* 1.3 59.2 + - - +
297A ALA* 3.4 4.3 + - - +
298A LEU* 3.0 35.1 + - + +
328A PHE* 5.0 0.2 - - - -
329A VAL* 3.7 27.1 - - + +
332A LEU* 3.8 27.4 - - + -
345A ILE* 4.2 23.6 - - + +
365A ARG* 3.8 36.6 - - - +
377A PHE* 5.2 1.1 - - + -
859A MET* 4.2 9.6 - - + -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 3.7 27.0 + - + +
294A VAL* 1.3 78.8 - - - +
296A THR* 1.3 57.0 + - - +
298A LEU* 3.4 8.4 + - + +
299A GLU* 3.0 73.3 + - + +
365A ARG* 4.5 17.9 - - - +
368A LEU* 3.7 22.2 - - + -
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Residues in contact with THR 296 (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 ARG* 5.1 13.0 - - - +
286A LEU* 4.0 20.0 - - + -
289A SER* 6.1 0.2 - - - +
290A SER* 4.0 21.6 + - - +
292A ASP 3.1 17.2 + - - -
293A PRO* 3.9 3.6 - - - -
294A VAL 3.3 0.2 - - - -
295A MET* 1.3 78.2 - - - +
297A ALA* 1.3 56.4 + - - +
299A GLU* 3.9 4.8 - - - +
300A LEU* 2.9 32.8 + - + +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.1 15.0 - - + +
293A PRO 2.9 19.9 + - - +
294A VAL 3.9 0.2 - - - +
296A THR* 1.3 76.5 - - - +
298A LEU* 1.3 58.4 + - - +
300A LEU* 3.8 5.5 - - - +
301A SER* 2.9 30.5 + - - -
325A CYS* 3.9 11.6 - - - +
328A PHE* 3.7 14.6 - - + -
329A VAL* 3.7 25.4 - - + -
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Residues in contact with LEU 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 VAL* 3.0 30.4 + - + +
295A MET* 3.8 8.5 - - + +
297A ALA* 1.3 77.1 - - - +
299A GLU* 1.3 60.9 + - - +
301A SER* 2.7 20.0 + - - +
302A ASN 3.0 6.4 + - - -
326A LYS* 6.2 0.7 - - + -
329A VAL* 4.7 17.0 - - + -
365A ARG* 4.0 33.2 - - + +
368A LEU* 4.8 13.7 - - + -
369A ALA* 4.8 11.4 - - + +
372A TYR* 3.5 23.5 - - + -
374A VAL* 3.8 31.6 - - + -
377A PHE* 5.9 2.9 - - + -
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MET* 3.0 48.2 + - + +
296A THR* 4.0 4.9 - - - +
298A LEU* 1.3 75.3 - - - +
300A LEU* 1.3 57.0 + - - +
302A ASN* 3.4 7.2 + - - +
303A GLU* 2.9 29.5 + - - +
368A LEU* 4.0 2.1 - - - +
372A TYR* 3.0 30.2 + - - -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 3.5 35.0 - - - +
277A TYR* 4.3 17.5 - - + -
280A LEU* 3.4 32.1 - - + +
281A ALA* 3.8 5.6 - - - -
286A LEU* 4.2 11.9 - - + -
296A THR* 2.9 20.3 + - + +
297A ALA* 3.9 3.6 - - - +
299A GLU* 1.3 74.7 - - - +
301A SER* 1.3 61.0 + - - +
303A GLU* 3.3 8.2 + - - +
304A LEU* 2.9 42.5 + - + +
325A CYS* 3.8 21.8 - - - -
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Residues in contact with SER 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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297A ALA 2.9 16.0 + - - -
298A LEU* 2.7 28.1 + - - +
300A LEU* 1.3 78.1 - - - +
302A ASN* 1.3 54.7 + - - +
305A ALA* 3.0 26.0 + - - +
322A SER* 3.0 29.2 + - - +
325A CYS* 3.8 19.7 - - - +
326A LYS* 4.2 18.4 - - - +
372A TYR* 4.8 4.1 - - - +
374A VAL* 4.8 3.3 - - - +
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Residues in contact with ASN 302 (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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298A LEU 3.0 9.4 + - - +
299A GLU* 3.7 11.6 + - - +
301A SER* 1.3 82.0 + - - +
303A GLU* 1.3 57.2 + - - +
305A ALA* 3.3 6.3 + - - +
306A VAL* 2.9 40.1 + - - +
372A TYR* 3.4 50.8 + - + -
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 2.7 35.5 + - - +
248A PRO 5.4 0.3 - - - +
277A TYR* 2.6 35.2 + - + +
299A GLU 2.9 17.7 + - - +
300A LEU* 3.3 8.7 + - + +
302A ASN* 1.3 78.0 - - - +
304A LEU* 1.3 58.2 + - - +
306A VAL* 3.3 6.0 + - - +
307A LEU* 3.0 39.6 + - + +
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Residues in contact with LEU 304 (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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277A TYR* 3.8 33.7 - - + -
281A ALA* 4.0 15.3 - - + -
300A LEU* 2.9 29.7 + - + +
303A GLU* 1.3 75.5 - - - +
305A ALA* 1.3 58.2 + - - +
307A LEU* 3.7 4.6 - - + +
308A ALA* 2.9 28.8 + - - +
318A TYR* 3.6 36.1 - - + +
321A LEU* 3.7 34.3 - - + +
322A SER* 3.9 15.3 - - - +
325A CYS* 4.0 7.0 - - - -
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Residues in contact with ALA 305 (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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301A SER 3.0 18.8 + - - +
302A ASN* 3.8 7.9 - - - +
304A LEU* 1.3 77.1 - - - +
306A VAL* 1.3 60.7 + - - +
308A ALA* 3.7 11.7 + - - +
309A ASN* 3.0 22.3 - - - +
318A TYR 5.5 0.2 - - - -
319A LYS* 4.9 11.6 + - + +
322A SER* 4.1 10.9 + - - +
326A LYS* 5.6 4.5 - - - +
372A TYR 6.0 2.5 - - - +
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Residues in contact with VAL 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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302A ASN* 2.9 34.7 + - - +
303A GLU* 3.6 8.1 - - - +
305A ALA* 1.3 77.4 - - + +
307A LEU* 1.3 64.0 + - + +
309A ASN* 3.1 8.8 + - - +
310A ILE* 3.0 47.5 + - + +
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Residues in contact with LEU 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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251A TYR* 5.4 11.4 - - + +
273A ARG* 3.7 17.3 - - - +
277A TYR* 3.7 33.9 - - + +
303A GLU* 3.0 36.7 + - + +
304A LEU* 3.4 7.4 + - + +
306A VAL* 1.3 83.0 - - + +
308A ALA* 1.3 60.9 + - - +
309A ASN 3.2 0.2 - - - -
310A ILE* 3.9 12.8 - - + +
311A GLU* 3.1 35.7 + - + +
318A TYR* 3.7 26.2 - - + +
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Residues in contact with ALA 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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304A LEU 2.9 17.0 + - - +
305A ALA* 3.8 9.4 - - - +
306A VAL 3.2 0.6 - - - -
307A LEU* 1.3 78.3 - - - +
309A ASN* 1.3 58.0 + - - +
311A GLU 3.5 9.9 - - - +
312A LYS* 4.8 1.2 - - - -
315A LYS* 3.4 31.5 - - + +
318A TYR* 3.7 21.5 - - + +
319A LYS* 4.0 28.3 - - + +
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Residues in contact with ASN 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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305A ALA 3.0 18.5 - - - +
306A VAL* 3.1 7.2 + - - +
308A ALA* 1.3 82.3 + - - +
310A ILE* 1.3 66.1 + - + +
311A GLU 4.5 2.6 - - - -
312A LYS* 4.6 4.9 + - - +
315A LYS* 5.2 5.4 - - - +
319A LYS* 4.4 16.5 + - - +
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Residues in contact with ILE 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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251A TYR* 3.6 27.5 - - + -
252A PHE* 3.6 36.4 - - + -
306A VAL* 3.0 38.5 + - + +
307A LEU* 4.3 11.0 - - + -
309A ASN* 1.3 80.0 - - + +
311A GLU* 1.3 58.2 + - + +
312A LYS* 3.6 3.8 + - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 3.3 44.9 + - + +
270A SER* 4.1 15.9 + - - -
273A ARG* 3.7 18.0 + - - -
307A LEU* 3.1 21.3 + - + +
308A ALA* 3.5 15.3 - - - +
309A ASN 4.5 0.2 - - - -
310A ILE* 1.3 75.5 - - + +
312A LYS* 1.3 59.4 + - - +
313A GLU* 2.9 30.3 - - + +
314A PHE* 3.8 17.0 - - - -
315A LYS* 4.4 1.6 + - - +
318A TYR* 3.9 18.2 + - + -
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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