Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 1RS0
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 ASN 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LYS* 4.3 7.2 - - - +
302A ALA 5.5 0.2 - - - +
303A ASP* 3.0 21.7 + - + +
304A SER 3.4 0.4 - - - -
305A SER* 1.3 75.3 + - - +
307A ALA* 1.3 62.5 + - - +
308A ASP* 2.9 24.7 + - - +
309A TRP* 2.8 27.3 + - + +
310A VAL* 3.0 14.2 + - - +
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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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272A ILE* 3.9 22.7 - - + +
276A ALA* 4.1 24.0 - - + -
281A LYS* 5.2 1.3 - - + +
284A TYR* 5.1 8.0 - - + -
305A SER 3.5 6.6 + - - +
306A ASN* 1.3 73.1 - - - +
308A ASP* 1.3 56.0 + - - +
310A VAL* 4.6 4.7 - - - -
311A THR* 2.7 38.4 + - - -
583A ARG* 5.5 4.9 - - - +
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Residues in contact with ASP 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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306A ASN* 2.9 12.4 + - - +
307A ALA* 1.3 79.1 - - - +
309A TRP* 1.3 58.4 + - - +
311A THR* 3.4 6.3 + - - +
312A LYS* 3.0 27.2 + - - +
583A ARG* 4.8 4.7 + - - +
683A ARG* 3.0 43.1 + - - -
743A NA 4.1 10.6 - - - -
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Residues in contact with TRP 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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296A TRP 4.7 2.5 - - - -
297A VAL* 3.8 28.3 - - + -
301A GLU* 3.7 27.4 - - - -
303A ASP* 3.2 56.1 + - + -
304A SER 4.2 1.1 - - - -
306A ASN* 2.8 27.8 + - + +
308A ASP* 1.3 74.6 - - - +
310A VAL* 1.3 76.4 + - + +
312A LYS* 3.0 14.0 + - + +
313A GLN* 2.9 61.6 + - + +
743A NA 3.8 16.5 - - - -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.9 3.1 - - + -
272A ILE* 4.1 19.1 - - + -
284A TYR* 4.0 28.9 - - + -
286A LEU* 4.8 13.7 - - + -
297A VAL* 4.6 8.7 - - + -
303A ASP 4.0 4.3 - - - +
304A SER* 3.4 31.4 - - - +
306A ASN 3.0 12.8 + - - +
307A ALA* 4.1 4.0 - - - +
309A TRP* 1.3 81.7 - - + +
311A THR* 1.3 62.4 + - - +
313A GLN* 3.3 9.8 + - - +
314A LEU* 3.0 22.2 + - - +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 4.5 21.7 + - + -
272A ILE* 3.6 23.0 - - - +
273A GLU* 5.5 0.3 + - - -
307A ALA 2.7 22.1 + - - -
308A ASP* 3.6 7.6 + - - -
309A TRP 3.1 0.2 - - - -
310A VAL* 1.3 73.5 - - - +
312A LYS* 1.3 66.9 + - - +
314A LEU* 3.3 7.0 + - - +
315A ASN* 2.9 38.5 + - - +
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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 ASP 3.0 13.7 + - - +
309A TRP* 3.0 16.4 + - + +
311A THR* 1.3 78.2 - - - +
313A GLN* 1.3 72.4 + - - +
315A ASN* 3.1 10.4 + - - +
316A GLU* 3.0 51.3 + - + +
743A NA 4.3 12.8 - - - -
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Residues in contact with GLN 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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286A LEU* 4.5 3.4 - - + -
296A TRP* 4.6 17.5 + - + +
297A VAL* 4.1 21.5 - - + -
309A TRP* 2.9 68.0 + - + +
310A VAL 3.6 4.9 - - - +
311A THR 3.3 0.2 - - - -
312A LYS* 1.3 87.8 - - - +
314A LEU* 1.3 62.5 + - - +
316A GLU* 3.0 28.1 + - - +
317A ILE* 3.2 17.1 + - - +
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Residues in contact with LEU 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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248A LEU* 4.9 2.9 - - + -
250A LEU* 5.2 2.7 - - + -
265A LYS* 3.2 47.2 + - + +
268A LEU* 3.7 29.6 - - + -
269A VAL* 3.5 30.1 - - + -
272A ILE* 3.8 17.7 - - + -
286A LEU* 3.8 30.2 - - + +
310A VAL 3.0 16.2 + - - +
311A THR* 3.7 5.2 - - - +
313A GLN* 1.3 76.8 - - - +
315A ASN* 1.3 60.1 + - - +
317A ILE* 3.5 12.0 + - + +
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Residues in contact with ASN 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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265A LYS* 3.6 14.7 + - - +
269A VAL* 3.8 25.1 - - - +
311A THR* 2.9 27.1 + - - +
312A LYS* 3.1 12.7 + - - +
314A LEU* 1.3 79.6 + - - +
316A GLU* 1.3 61.5 + - + +
317A ILE 3.5 1.2 + - - +
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Residues in contact with GLU 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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296A TRP* 5.0 5.1 - - + -
312A LYS* 3.0 48.1 + - + +
313A GLN* 3.0 21.8 + - - +
315A ASN* 1.3 77.1 - - + +
317A ILE* 1.3 63.4 + - - +
318A ASN* 3.3 5.4 + - - +
321A ASP* 3.8 7.6 - - - +
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Residues in contact with ILE 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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250A LEU* 6.4 0.4 - - + -
261A PHE* 3.8 27.8 - - + -
265A LYS* 2.8 31.9 + - + -
286A LEU* 3.7 33.4 - - + -
288A THR* 4.2 10.1 - - + -
296A TRP* 3.6 48.0 - - + +
313A GLN 3.3 10.5 - - - +
314A LEU* 3.6 18.4 - - + +
315A ASN 3.2 2.0 - - - +
316A GLU* 1.3 76.7 - - - +
318A ASN* 1.3 64.0 + - - +
319A TYR 4.3 0.3 + - - -
321A ASP* 4.1 3.4 - - - -
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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