Contacts of the helix formed by residues 301 - 317 (chain A) in PDB entry 3RU0
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 LYS 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A LEU* 2.9 29.4 + - + +
299A HIS* 3.6 29.5 + - + +
300A TRP* 1.3 73.9 - - - +
302A TRP* 1.3 64.8 + - - +
303A GLU 3.4 2.5 - - - -
304A GLN* 3.2 32.1 + - - +
305A VAL* 3.1 24.7 + - - +
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Residues in contact with TRP 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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191A GLN* 3.7 26.9 - - + -
297A LYS* 3.7 26.2 - - + -
300A TRP* 3.2 56.4 + + - +
301A LYS* 1.3 69.2 - - - +
303A GLU* 1.3 60.0 + - - +
305A VAL* 4.3 8.5 - - + -
306A LEU* 2.9 29.6 + - - +
333A CYS 5.2 1.6 - - - -
336A ASP* 4.5 7.9 - - + -
337A ALA* 3.5 31.1 - - + +
340A ASN* 3.4 49.7 + - + +
341A LEU* 3.9 24.9 - - + +
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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
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301A LYS 3.4 0.6 - - - -
302A TRP* 1.3 77.1 - - - +
304A GLN* 1.3 61.6 + - + +
306A LEU* 3.5 2.9 + - - +
307A ALA* 3.0 28.4 + - - +
341A LEU* 3.7 28.5 - - + -
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Residues in contact with GLN 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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296A LEU* 3.4 30.6 - - + +
301A LYS* 3.2 38.3 + - + +
303A GLU* 1.3 76.9 - - + +
305A VAL* 1.3 64.8 + - - +
307A ALA* 3.7 5.5 - - - +
308A MET* 3.1 29.1 + - - +
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Residues in contact with VAL 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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293A ILE* 3.8 10.1 - - + +
296A LEU* 3.5 25.1 - - + -
297A LYS* 3.5 22.7 - - + +
301A LYS 3.1 16.4 + - - +
302A TRP* 3.7 13.7 - - + +
304A GLN* 1.3 73.1 - - - +
306A LEU* 1.3 66.0 + - - +
308A MET* 3.2 4.6 + - - +
309A CYS* 3.0 36.1 + - - -
333A CYS* 3.8 31.6 - - + +
337A ALA* 4.0 3.4 - - + -
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Residues in contact with LEU 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 TRP 2.9 18.3 + - - +
303A GLU* 3.7 4.9 - - - +
305A VAL* 1.3 77.5 - - - +
307A ALA* 1.3 62.6 + - - +
309A CYS* 3.3 3.3 + - - -
310A GLN* 2.9 57.5 + - + +
334A ALA* 4.1 14.1 - - + +
337A ALA* 4.0 6.5 - - + -
338A CYS* 3.6 24.9 - - - -
341A LEU* 3.8 13.0 - - + -
343A LEU* 3.6 30.5 - - + -
346A GLU* 4.1 1.8 - - - +
350A TYR* 4.4 5.4 - - + -
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Residues in contact with ALA 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 GLU 3.0 17.9 + - - +
304A GLN* 3.7 7.4 - - - +
305A VAL 3.3 0.2 - - - -
306A LEU* 1.3 77.4 - - - +
308A MET* 1.3 64.4 + - + +
310A GLN* 4.0 11.1 - - - +
311A ALA* 3.4 20.1 + - - +
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Residues in contact with MET 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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289A SER* 3.8 22.7 - - - +
292A LYS* 3.6 28.9 - - + -
293A ILE* 3.6 29.2 - - + -
296A LEU* 3.8 15.0 - - + -
304A GLN 3.1 13.6 + - - +
305A VAL 3.7 3.6 - - - +
307A ALA* 1.3 82.7 - - + +
309A CYS* 1.3 61.3 + - - +
311A ALA* 3.5 6.6 + - - +
312A ILE* 3.3 26.2 + - + +
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Residues in contact with CYS 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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293A ILE* 3.8 26.9 - - - -
305A VAL* 3.0 24.4 + - - +
306A LEU 3.8 3.4 - - - +
308A MET* 1.3 73.6 - - - +
310A GLN* 1.3 60.4 + - - +
312A ILE* 3.1 4.2 + - - +
313A ILE* 2.8 35.1 + - - +
330A VAL* 3.6 36.3 - - + -
333A CYS* 3.9 9.6 - - - -
334A ALA* 3.8 20.4 - - + -
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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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306A LEU* 2.9 43.8 + - + +
307A ALA* 4.0 10.1 - - - +
309A CYS* 1.3 76.3 - - - +
311A ALA* 1.3 58.1 + - - +
313A ILE* 4.0 6.7 - - - +
314A SER* 2.8 35.1 + - - -
346A GLU* 2.7 28.2 + - - +
350A TYR* 3.6 18.2 - - + +
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Residues in contact with ALA 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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307A ALA 3.4 11.7 + - - +
308A MET* 3.6 11.0 - - - +
309A CYS 3.2 0.4 - - - -
310A GLN* 1.3 77.8 - - - +
312A ILE* 1.3 61.1 + - + +
314A SER* 3.3 6.2 + - - -
315A SER* 3.1 29.2 + - - -
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Residues in contact with ILE 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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285A GLU 6.4 0.2 - - - -
286A VAL* 4.1 22.9 - - + -
289A SER* 3.4 35.2 - - - +
293A ILE* 3.6 22.7 - - + -
308A MET* 3.3 11.6 + - + +
309A CYS 3.1 7.4 + - - +
311A ALA* 1.3 76.2 - - + +
313A ILE* 1.3 65.4 + - - +
315A SER* 3.4 4.9 + - - -
316A ASN* 2.9 44.9 + - - +
327A GLN* 4.4 6.3 - - - +
330A VAL* 4.1 19.7 - - + -
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Residues in contact with ILE 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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309A CYS 2.8 25.9 + - - +
310A GLN* 4.0 3.8 - - - +
312A ILE* 1.3 70.4 - - - +
314A SER* 1.3 63.1 + - - +
316A ASN* 4.1 0.9 - - - +
317A SER* 3.4 24.1 + - - -
327A GLN* 3.8 23.2 - - - +
330A VAL* 3.8 9.6 - - + -
331A LEU* 3.8 13.0 - - + -
334A ALA* 3.9 18.2 - - + -
349A PHE* 5.3 1.1 - - + -
350A TYR* 3.6 32.5 - - + +
353A ARG* 3.6 35.1 + - - +
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Residues in contact with SER 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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310A GLN 2.8 23.4 + - - -
311A ALA* 3.3 7.3 + - - -
313A ILE* 1.3 78.3 - - - +
315A SER* 1.3 64.0 + - - +
317A SER* 3.2 19.9 + - - -
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Residues in contact with SER 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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311A ALA 3.1 20.0 + - - -
312A ILE* 3.4 6.8 + - - -
313A ILE 3.3 0.2 - - - -
314A SER* 1.3 79.5 + - - +
316A ASN* 1.3 69.3 + - - +
317A SER 3.5 0.7 + - - -
318A GLU* 5.0 2.6 + - - +
319A ARG* 3.1 19.7 + - - -
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Residues in contact with ASN 316 (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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282A VAL* 3.3 28.0 - - - +
286A VAL* 3.9 13.8 - - - +
312A ILE* 2.9 41.9 + - - +
313A ILE 4.1 0.9 - - - +
314A SER 3.3 0.2 - - - -
315A SER* 1.3 85.2 + - - +
317A SER* 1.3 60.2 + - - +
318A GLU 3.2 2.9 - - - -
319A ARG* 3.0 15.1 + - - +
320A LEU* 2.8 38.6 + - + +
327A GLN* 3.7 16.2 - - - +
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Residues in contact with SER 317 (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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313A ILE* 3.4 16.8 + - - -
314A SER* 3.2 14.3 + - - -
315A SER 3.5 1.2 - - - -
316A ASN* 1.3 77.6 - - - +
318A GLU* 1.3 69.4 + - - +
319A ARG 3.6 0.2 + - - -
320A LEU 4.7 6.2 + - - +
353A ARG* 5.7 8.7 - - - +
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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
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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