Contacts of the helix formed by residues 241 - 255 (chain A) in PDB entry 1SVS
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A TYR 2.9 25.8 + - - +
231A ASP* 4.6 2.8 - - - +
232A LEU 3.5 11.3 + - - -
233A VAL* 4.5 3.8 - - - +
239A GLU 4.0 2.4 + - - -
240A MET* 1.3 79.9 - - - +
242A ARG* 1.3 65.0 + - - +
243A MET* 2.8 33.7 + - - +
244A HIS* 3.0 40.2 + - + +
245A GLU 3.1 16.8 + - - -
285A ILE* 4.4 8.9 + - - +
286A CYS* 3.8 10.3 - - - +
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Residues in contact with ARG 242 (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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42A GLY 5.5 2.9 - - - -
43A GLU* 4.1 28.5 - - - +
147A GLN* 2.7 30.3 + - - +
148A LEU 6.0 0.4 - - - +
150A ASP* 5.5 4.0 + - - -
229A ASP* 3.1 52.4 + - - +
232A LEU* 2.9 32.2 + - - +
233A VAL 3.0 29.2 + - - -
234A LEU* 3.6 23.2 - - + +
235A ALA* 4.9 3.8 - - - +
240A MET 3.4 0.8 + - - -
241A ASN* 1.3 71.9 + - - +
243A MET* 1.3 63.4 + - - +
245A GLU* 3.3 4.9 + - - +
246A SER* 3.0 20.8 + - - -
270A LYS* 5.6 0.8 - - - +
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Residues in contact with MET 243 (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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225A VAL* 4.3 9.9 - - + -
226A ALA 3.5 16.2 - - - +
227A LEU* 3.4 31.6 - - - +
229A ASP* 3.8 4.1 + - + +
230A TYR* 3.9 21.8 - - + +
241A ASN* 2.8 14.0 + - - +
242A ARG* 1.3 72.9 - - - +
244A HIS* 1.3 66.5 + - - +
246A SER* 3.2 6.6 + - - -
247A MET* 2.9 23.1 + - - +
286A CYS* 3.7 8.1 - - - -
287A TYR* 3.5 39.3 - - - +
303A ILE* 4.0 20.9 - - + -
307A PHE* 4.1 8.7 - - + -
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Residues in contact with HIS 244 (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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240A MET* 4.4 11.0 - - - -
241A ASN* 3.0 32.9 + - + +
243A MET* 1.3 76.2 - - - +
245A GLU* 1.3 63.5 + - - +
247A MET* 3.2 18.5 + - - +
248A LYS* 3.1 33.6 + - - +
285A ILE 5.4 1.8 - - - -
286A CYS* 2.9 46.4 + - - -
287A TYR* 5.0 2.7 - + - -
288A PRO* 6.0 0.9 - - + -
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Residues in contact with GLU 245 (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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41A ALA* 4.8 2.5 - - + -
205A ARG* 2.8 33.5 + - - -
208A ARG* 2.7 46.0 + - - +
234A LEU* 3.2 24.3 - - + +
240A MET* 3.7 12.6 - - + +
241A ASN 3.1 11.7 + - - +
242A ARG 3.4 9.9 - - - +
244A HIS* 1.3 78.4 - - - +
246A SER* 1.3 62.6 + - - +
248A LYS* 3.2 15.1 + - - +
249A LEU* 3.1 23.7 + - + +
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Residues in contact with SER 246 (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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41A ALA* 4.7 11.9 + - - +
223A PHE* 3.8 6.5 - - - -
224A CYS 4.6 1.0 + - - -
225A VAL* 3.3 36.5 - - - +
226A ALA 5.9 0.4 - - - -
229A ASP* 6.1 0.9 - - - -
242A ARG 3.0 13.4 + - - -
243A MET* 3.2 11.9 + - - -
245A GLU* 1.3 77.8 - - - +
247A MET* 1.3 57.5 + - - +
249A LEU* 3.2 13.3 + - - +
250A PHE* 2.9 28.2 + - - +
307A PHE* 3.5 7.4 - - - -
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Residues in contact with MET 247 (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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243A MET 2.9 18.1 + - - +
244A HIS* 3.5 18.8 - - - +
246A SER* 1.3 77.2 - - - +
248A LYS* 1.3 56.9 + - + +
250A PHE 3.2 0.3 + - - -
251A ASP* 2.9 31.1 + - - +
287A TYR* 3.2 28.3 - - + -
306A GLN* 3.8 41.5 - - + +
307A PHE* 3.4 28.5 - - + -
310A LEU* 3.4 22.8 - - + +
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Residues in contact with LYS 248 (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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240A MET* 3.2 31.5 - - - +
244A HIS* 3.1 19.8 + - - +
245A GLU* 3.2 17.9 + - - +
247A MET* 1.3 77.0 - - + +
249A LEU* 1.3 64.1 + - + +
251A ASP* 3.4 6.8 + - - +
252A SER* 3.1 22.2 + - - -
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Residues in contact with LEU 249 (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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41A ALA* 3.9 28.0 - - + +
208A ARG* 3.7 53.4 - - - +
211A TRP* 4.2 18.6 - - + -
223A PHE* 3.8 12.6 - - + -
245A GLU* 3.1 16.9 + - + +
246A SER* 3.6 7.4 - - - +
248A LYS* 1.3 76.5 - - + +
250A PHE* 1.3 65.2 + - - +
252A SER* 3.2 8.1 + - - -
253A ILE* 3.0 27.0 + - - +
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Residues in contact with PHE 250 (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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223A PHE* 3.5 39.4 - + + -
246A SER 2.9 16.8 + - - +
247A MET 3.7 3.8 - - - +
249A LEU* 1.3 73.6 - - - +
251A ASP* 1.3 60.4 + - - +
253A ILE* 4.5 1.1 - - + +
254A CYS* 2.8 53.8 + - + +
264A ILE* 3.9 22.7 - - + -
266A LEU* 4.0 17.3 - - + -
307A PHE* 3.5 47.8 - + + -
310A LEU* 4.1 8.3 - - + -
311A ASN 5.4 0.4 - - - -
319A ILE* 3.6 35.0 - - + -
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Residues in contact with ASP 251 (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 MET 2.9 17.1 + - - +
248A LYS* 3.5 9.4 - - - +
250A PHE* 1.3 77.2 - - - +
252A SER* 1.3 61.7 + - - +
254A CYS* 5.0 0.2 - - - -
255A ASN* 2.8 36.4 + - - +
310A LEU* 4.2 27.8 - - + +
312A LYS* 2.6 32.6 + - - -
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Residues in contact with SER 252 (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 LYS 3.1 10.7 + - - -
249A LEU* 3.5 12.8 - - - -
250A PHE 3.2 0.2 - - - -
251A ASP* 1.3 80.2 - - - +
253A ILE* 1.3 66.0 + - - +
255A ASN* 4.0 0.9 - - - +
256A ASN* 3.3 26.6 + - - +
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Residues in contact with ILE 253 (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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39A LEU* 3.7 25.4 - - + -
211A TRP* 4.1 19.5 - - + -
215A PHE* 4.1 23.1 - - + -
221A ILE* 3.7 34.1 - - + -
223A PHE* 4.2 13.9 - - + -
249A LEU 3.0 15.7 + - - +
250A PHE* 4.0 3.1 - - + +
252A SER* 1.3 80.2 - - - +
254A CYS* 1.3 69.2 + - - +
256A ASN* 3.1 21.2 + - - +
259A PHE* 3.7 12.8 - - + +
264A ILE* 4.7 5.3 - - + +
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Residues in contact with CYS 254 (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 PHE* 2.8 40.2 + - + +
251A ASP* 4.5 1.1 - - - +
253A ILE* 1.3 78.3 - - - +
255A ASN* 1.3 62.5 + - - +
256A ASN 3.6 3.5 + - - +
259A PHE* 5.5 1.0 - - - +
264A ILE* 4.5 14.9 - - + +
310A LEU 5.9 0.4 - - - -
311A ASN* 4.3 21.0 - - - +
317A LYS* 4.3 24.3 - - - +
319A ILE* 3.7 35.4 - - - -
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Residues in contact with ASN 255 (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 ASP* 2.8 41.4 + - - +
252A SER* 4.0 1.8 - - - +
253A ILE 3.2 0.8 - - - -
254A CYS* 1.3 79.4 - - - +
256A ASN* 1.3 62.4 + - - +
257A LYS* 3.2 5.4 + - - +
310A LEU 2.9 19.8 + - - -
311A ASN* 3.8 7.7 - - - +
312A LYS* 2.8 48.4 + - + +
313A ARG* 4.4 3.1 + - - +
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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
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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