Contacts of the helix formed by residues 246 - 263 (chain A) in PDB entry 1N35
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A GLY 3.7 0.8 + - - -
245A LEU* 1.3 70.1 - - - +
247A PRO* 1.3 75.9 - - - +
248A SER* 2.8 24.5 + - - -
249A LEU* 3.1 17.0 + - + +
250A VAL* 3.1 21.9 + - - +
350A ARG* 2.8 27.6 + - - -
367A ASP* 2.9 15.5 + - - +
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Residues in contact with PRO 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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179A PRO* 4.2 24.9 - - + -
183A HIS* 4.6 8.1 - - + +
185A CYS* 5.5 0.3 - - - +
240A GLN* 3.6 36.3 - - + +
245A LEU 3.3 7.8 - - - +
246A ASP* 1.3 91.2 - - - +
248A SER* 1.3 61.3 + - - +
250A VAL* 3.1 3.6 + - - +
251A LYS* 3.0 30.0 + - + +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP* 2.8 22.1 + - - -
247A PRO* 1.3 79.9 - - - +
249A LEU* 1.3 60.5 + - - +
251A LYS* 3.6 16.8 + - - +
252A LEU* 3.5 16.5 + - - +
350A ARG* 2.9 28.8 + - - -
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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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245A LEU* 6.3 0.2 - - + -
246A ASP* 3.1 18.9 + - + +
248A SER* 1.3 79.9 + - - +
250A VAL* 1.3 57.5 + - - +
252A LEU* 2.7 49.6 + - + +
253A GLY 3.2 4.2 + - - -
277A PHE* 4.6 2.1 - - + -
347A LEU* 3.9 15.9 - - + -
350A ARG* 3.6 26.5 - - - +
364A TYR* 3.9 26.5 - - + +
367A ASP* 3.7 29.2 - - + +
368A ALA* 3.8 16.8 - - + +
371A CYS* 3.9 13.5 - - - +
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Residues in contact with VAL 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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185A CYS* 5.4 0.4 - - + -
186A PRO* 3.4 34.5 - - + -
236A LEU* 4.3 16.4 - - + +
240A GLN* 3.4 22.2 - - + +
245A LEU* 3.9 30.7 - - + -
246A ASP 3.1 16.2 - - - +
247A PRO 3.1 7.4 + - - +
249A LEU* 1.3 76.9 - - - +
251A LYS* 1.3 62.6 + - - +
253A GLY* 2.9 12.8 + - - -
254A VAL* 2.9 11.1 + - - +
371A CYS* 3.7 10.8 - - - -
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Residues in contact with LYS 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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53A ASP 4.9 0.2 + - - -
54A ASP* 3.1 27.2 + - - +
56A MET 3.0 27.5 + - - -
57A LEU* 3.9 18.8 - - + +
185A CYS* 3.8 22.7 - - + -
247A PRO* 3.0 20.7 + - + +
248A SER* 3.7 14.4 - - - +
249A LEU 3.1 0.4 - - - -
250A VAL* 1.3 75.8 - - - +
252A LEU* 1.3 63.9 + - + +
254A VAL* 3.0 12.3 + - - +
255A GLN* 2.9 33.3 + - - +
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Residues in contact with LEU 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 SER 3.5 10.8 - - - +
249A LEU* 2.7 33.3 + - + +
251A LYS* 1.3 74.8 - - + +
253A GLY* 1.3 58.3 + - - -
255A GLN* 3.3 23.6 + - - +
256A ILE* 3.2 26.2 + - - +
277A PHE* 3.8 12.8 - - + -
342A SER 5.7 0.2 - - - +
343A VAL* 4.1 22.5 - - + +
346A GLU* 4.3 25.1 - - + -
347A LEU* 3.5 34.3 - - + -
350A ARG* 5.0 2.5 - - - +
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Residues in contact with GLY 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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236A LEU* 4.3 6.3 - - - -
249A LEU 3.2 3.8 + - - -
250A VAL 2.9 8.6 + - - -
252A LEU* 1.3 80.8 - - - +
254A VAL* 1.3 60.8 + - - +
256A ILE* 3.5 4.3 + - - +
257A CYS* 3.2 27.2 + - - -
277A PHE* 3.6 12.2 - - - -
371A CYS* 3.7 24.4 - - - +
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Residues in contact with VAL 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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57A LEU* 4.1 7.0 - - + -
185A CYS* 4.4 4.7 - - - -
186A PRO* 3.8 32.8 - - + -
189A CYS* 3.6 28.5 - - - -
233A LEU* 3.9 19.5 - - + -
236A LEU* 4.1 5.4 - - + -
250A VAL 2.9 16.3 + - - +
251A LYS* 3.0 10.2 + - - +
253A GLY* 1.3 75.2 - - - +
255A GLN* 1.3 54.0 + - - +
257A CYS* 3.1 7.9 + - - +
258A LEU* 2.7 46.0 + - + +
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Residues in contact with GLN 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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57A LEU* 3.8 19.0 - - + +
251A LYS* 2.9 20.2 + - - +
252A LEU* 3.5 25.9 - - - +
254A VAL* 1.3 76.3 - - - +
256A ILE* 1.3 63.3 + - - +
258A LEU* 3.1 10.3 + - + +
259A HIS* 2.8 42.7 + - + +
340A LEU* 5.2 0.4 - - - -
342A SER* 4.8 9.0 + - - -
343A VAL* 3.6 24.6 - - + +
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Residues in contact with ILE 256 (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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252A LEU 3.2 9.3 + - - +
253A GLY* 3.7 6.5 - - - +
254A VAL 3.2 0.2 - - - -
255A GLN* 1.3 75.4 - - - +
257A CYS* 1.3 59.0 + - - +
259A HIS* 3.0 10.1 + - - +
260A ALA* 2.8 26.2 + - - +
269A PHE* 4.0 2.9 - - + -
270A ILE* 4.6 11.9 - - + -
273A THR* 3.9 23.1 - - - +
276A ILE* 4.1 24.2 - - + -
277A PHE* 3.3 39.5 - - + -
340A LEU* 4.2 21.3 - - + -
343A VAL* 4.3 10.5 - - + -
371A CYS 5.9 0.2 - - - +
373A SER 6.3 1.1 - - - +
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Residues in contact with CYS 257 (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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229A LEU* 3.6 14.3 - - + +
232A ASP* 3.6 23.1 - - + -
233A LEU* 5.0 2.9 - - + -
236A LEU* 4.6 8.5 - - - -
253A GLY 3.2 16.6 - - - -
254A VAL* 3.1 10.4 + - - +
256A ILE* 1.3 79.5 - - - +
258A LEU* 1.3 56.9 + - - +
260A ALA* 3.1 4.5 + - - -
261A ALA* 2.9 26.3 + - - +
266A TYR* 3.3 31.8 - - - +
270A ILE* 5.0 2.5 - - - -
371A CYS 5.2 1.1 - - - -
373A SER* 4.8 11.9 - - - -
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Residues in contact with LEU 258 (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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57A LEU* 4.3 11.9 - - + -
58A PRO 3.9 12.6 - - - +
59A ILE* 4.1 13.5 - - + -
60A PRO* 3.9 27.3 - - + +
63A ILE* 3.4 24.0 - - + +
189A CYS* 4.8 2.0 - - + -
193A ILE* 4.0 23.1 - - + -
229A LEU* 4.2 10.5 - - + -
233A LEU* 5.4 0.4 - - + -
254A VAL* 2.7 38.2 + - + +
255A GLN* 3.5 9.9 - - + +
257A CYS* 1.3 72.0 - - - +
259A HIS* 1.3 59.9 + - - +
261A ALA* 3.3 1.3 + - - -
262A ALA* 2.8 29.6 + - - +
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO* 5.5 6.8 - - + +
255A GLN* 2.8 38.9 + - + +
256A ILE 3.3 8.5 - - - +
258A LEU* 1.3 75.7 - - + +
260A ALA* 1.3 60.9 + - - +
262A ALA* 3.1 8.4 + - + +
263A SER* 2.9 29.1 + - - -
269A PHE* 3.7 18.9 - + + -
338A TYR 4.3 4.0 - - - -
339A GLY* 3.0 31.0 + - - -
340A LEU* 3.2 16.5 - - + +
343A VAL* 6.2 0.4 - - + -
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Residues in contact with ALA 260 (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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96A ASN* 3.0 10.0 + - - -
256A ILE 2.8 10.7 + - - +
257A CYS 3.1 6.7 + - - +
259A HIS* 1.3 78.3 - - - +
261A ALA* 1.3 56.3 - - - +
263A SER* 2.7 19.8 + - - -
266A TYR* 3.3 33.8 - - + +
269A PHE* 3.4 26.2 - - + -
270A ILE* 3.7 17.7 - - + -
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Residues in contact with ALA 261 (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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63A ILE* 3.7 28.5 - - + +
66A LYS* 3.8 10.4 - - - -
96A ASN* 3.2 15.4 + - - +
223A THR* 5.4 0.3 - - - +
225A ALA* 4.3 11.7 - - + +
226A ILE* 5.6 0.7 - - + -
229A LEU* 4.1 19.5 - - + -
257A CYS 2.9 15.4 + - - +
258A LEU 3.7 4.5 - - - +
260A ALA* 1.3 76.9 - - - +
262A ALA* 1.3 58.9 + - - +
263A SER 3.8 0.5 - - - +
266A TYR* 3.3 14.5 - - + -
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Residues in contact with ALA 262 (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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60A PRO* 4.1 11.0 - - + -
62A THR* 4.0 20.7 + - - +
63A ILE* 3.7 11.4 - - + +
66A LYS* 2.9 20.2 + - - +
258A LEU 2.8 15.7 + - - +
259A HIS* 3.1 9.8 + - + +
261A ALA* 1.3 76.3 - - - +
263A SER* 1.3 61.9 + - - +
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Residues in contact with SER 263 (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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66A LYS* 3.0 11.5 + - - -
96A ASN* 2.7 16.8 + - - -
259A HIS 2.9 13.2 + - - -
260A ALA 2.7 19.2 + - - -
261A ALA 3.3 0.4 - - - -
262A ALA* 1.3 83.6 - - - +
264A SER* 1.3 59.1 + - - +
265A SER 3.1 18.3 + - - -
268A TRP* 5.4 4.7 - - - -
269A PHE* 3.5 24.9 - - - +
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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