Contacts of the helix formed by residues 253 - 271 (chain H) in PDB entry 1R4N
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 253 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H ASP* 2.8 34.0 + - + +
252H ASP* 1.3 73.6 - - - +
254H PRO* 1.3 58.7 - - - +
255H GLU* 3.1 29.6 + - - +
256H HIS* 2.6 52.5 + - + +
257H ILE* 3.3 4.3 + - - +
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Residues in contact with PRO 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLN* 5.7 6.1 - - - +
252H ASP 2.9 18.0 - - - +
253H ASP* 1.3 78.4 - - - +
255H GLU* 1.3 57.9 + - + +
256H HIS 2.8 1.0 + - - -
257H ILE* 2.9 6.7 + - + +
258H GLN* 2.6 37.4 + - - +
278H TYR* 3.8 17.2 + - - +
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Residues in contact with GLU 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU* 5.1 3.2 - - - +
243H PHE* 3.4 32.1 - - + -
253H ASP* 3.0 13.7 + - - +
254H PRO* 1.3 80.8 - - + +
256H HIS* 1.3 55.5 + - - +
258H GLN* 3.7 9.1 - - - +
259H TRP* 3.1 20.6 + - - +
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Residues in contact with HIS 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H TRP* 3.5 14.8 - + - -
243H PHE* 3.2 40.3 - + - +
247H VAL* 5.0 6.2 - - + +
248H PRO 3.5 14.1 - - - -
249H LEU* 3.8 10.5 - - + -
250H ASP* 2.8 52.1 + - + +
253H ASP* 2.6 33.8 + - + +
255H GLU* 1.3 70.3 - - - +
257H ILE* 1.3 60.1 + - + +
259H TRP* 3.1 4.9 + - - +
260H ILE* 2.8 34.3 + - - +
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Residues in contact with ILE 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H LEU* 6.1 0.2 - - + -
251H GLY* 2.8 32.8 - - - +
252H ASP 4.7 7.4 - - - +
253H ASP 4.2 4.9 - - - +
254H PRO* 2.9 6.6 + - + +
256H HIS* 1.3 73.0 - - + +
258H GLN* 1.3 57.5 + - - +
260H ILE* 2.9 8.7 + - + -
261H PHE* 2.5 37.8 + - - +
278H TYR* 3.3 27.6 - - + +
281H THR* 4.0 18.8 - - + +
282H GLN* 3.6 41.5 - - + +
285H VAL* 5.0 9.0 - - + -
286H LYS* 4.3 4.3 - - + -
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Residues in contact with GLN 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU* 3.6 27.9 - - + +
254H PRO 2.6 21.2 + - - +
255H GLU* 3.7 11.0 - - - +
257H ILE* 1.3 72.2 - - - +
259H TRP* 1.3 56.8 + - - +
261H PHE* 3.4 24.1 - - - +
262H GLN* 2.9 41.6 + - - +
278H TYR* 3.7 20.2 - - + +
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Residues in contact with TRP 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 4.2 22.0 - - - +
232H VAL* 4.0 20.2 - - + -
236H GLN* 3.8 27.8 - - + -
237H TRP* 3.5 26.9 - + + -
240H GLU* 4.3 14.3 + - + -
242H PRO* 3.3 38.3 + - + +
243H PHE* 4.4 13.0 - + + -
255H GLU 3.1 15.6 + - - +
256H HIS 3.3 6.7 - - - +
257H ILE 3.1 0.6 - - - -
258H GLN* 1.3 74.3 - - - +
260H ILE* 1.3 70.6 + - + +
262H GLN* 2.9 9.7 + - + +
263H LYS* 2.8 66.1 + - + +
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Residues in contact with ILE 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H ILE* 4.2 4.7 - - + +
232H VAL* 3.5 27.6 - - + +
233H ARG* 4.7 3.8 - - + +
237H TRP* 4.4 0.7 - - + -
249H LEU* 3.3 46.2 - - + -
256H HIS 2.8 21.2 + - - +
257H ILE* 3.5 7.9 - - - +
259H TRP* 1.3 88.9 - - + +
261H PHE* 1.3 52.3 + - - +
264H SER* 2.7 46.1 + - - +
281H THR* 3.7 16.8 - - + -
285H VAL* 3.9 22.9 - - + -
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Residues in contact with PHE 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 6.1 4.5 - - + -
257H ILE 2.5 20.7 + - - +
258H GLN* 3.4 26.2 - - - +
260H ILE* 1.3 72.4 - - - +
262H GLN* 1.3 57.5 + - - +
264H SER* 3.0 4.5 + - - -
265H LEU* 2.7 61.5 + - + +
276H VAL* 3.7 21.3 - - + -
277H THR* 3.5 5.6 - - - -
278H TYR* 3.2 46.4 - + + -
281H THR* 3.0 31.8 - - + +
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Residues in contact with GLN 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 3.4 25.9 + - - -
67C GLY* 4.1 9.0 + - - +
68C GLU* 4.9 2.8 - - - +
14D GLU* 3.9 33.0 - - - +
15D GLY* 5.2 4.2 - - - -
258H GLN* 2.9 27.4 + - - +
259H TRP* 3.2 12.6 - - + +
261H PHE* 1.3 78.9 - - - +
263H LYS* 1.3 62.6 + - + +
265H LEU* 3.1 19.0 - - - +
266H GLU* 3.0 50.0 + - - +
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Residues in contact with LYS 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C SER* 4.3 17.9 + - - +
18D ASN* 5.4 6.9 - - - +
232H VAL* 3.3 22.3 - - + +
236H GLN* 3.0 34.0 + - - +
240H GLU* 5.1 5.5 + - - -
259H TRP* 2.8 56.0 + - + +
262H GLN* 1.3 71.7 - - + +
264H SER* 1.3 61.8 + - - +
265H LEU 3.1 1.6 - - - -
266H GLU* 3.3 33.1 + - - +
267H ARG* 2.9 23.9 + - - +
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Residues in contact with SER 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H CYS* 3.8 3.7 - - - +
229H ILE* 3.0 48.4 - - - +
232H VAL* 3.3 15.6 - - - +
260H ILE* 2.7 30.2 + - - +
261H PHE* 3.5 4.5 - - - -
263H LYS* 1.3 74.3 - - - +
265H LEU* 1.3 57.4 + - - +
267H ARG* 3.7 3.4 - - - +
268H ALA* 2.8 31.4 + - - +
276H VAL* 4.2 7.2 - - - +
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Residues in contact with LEU 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN* 5.0 20.4 - - + +
65C VAL 5.4 3.6 - - - +
66C SER* 5.2 14.6 - - - -
81C ILE* 6.2 2.7 - - + -
261H PHE* 2.7 48.1 + - + +
262H GLN* 3.1 29.4 - - - +
264H SER* 1.3 78.5 - - - +
266H GLU* 1.3 58.9 + - + +
268H ALA* 3.7 5.0 + - + +
269H SER* 3.3 20.6 + - - -
276H VAL* 4.3 15.7 - - + +
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Residues in contact with GLU 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C SER* 5.9 0.7 - - - +
68C GLU* 4.2 18.8 - - - +
445C VAL* 5.1 11.5 - - - +
446C SER* 5.3 1.9 + - - -
18D ASN* 5.2 4.2 + - - -
262H GLN* 3.0 39.6 + - - +
263H LYS* 3.6 37.1 + - - +
265H LEU* 1.3 75.6 - - + +
267H ARG* 1.3 64.1 + - - +
269H SER* 3.1 10.2 + - - -
270H GLN* 3.1 27.6 + - + +
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Residues in contact with ARG 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H ILE 2.9 22.2 + - - -
219H ALA* 3.6 18.2 + - - +
222H PRO* 3.8 17.7 - - - +
227H HIS 3.9 6.7 + - - -
228H CYS* 3.9 15.3 - - + +
231H TYR* 2.9 60.1 + - + +
232H VAL* 4.5 4.0 - - + -
236H GLN* 5.2 1.8 - - - +
263H LYS 2.9 17.4 + - - +
264H SER* 3.7 6.3 - - - +
266H GLU* 1.3 74.2 - - - +
268H ALA* 1.3 67.3 + - - +
270H GLN* 3.0 40.4 + - - +
271H TYR* 3.3 25.4 + - + -
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Residues in contact with ALA 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H CYS* 3.3 17.2 - - - -
264H SER 2.8 18.3 + - - +
265H LEU* 3.7 7.2 - - + +
267H ARG* 1.3 77.4 - - - +
269H SER* 1.3 52.7 + - - +
271H TYR 3.3 1.2 - - - -
272H ASN 2.6 30.5 + - - -
273H ILE* 2.7 33.3 + - - +
276H VAL* 3.6 20.0 - - + -
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Residues in contact with SER 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASN* 4.4 12.5 + - - -
265H LEU* 3.3 12.1 + - - -
266H GLU* 3.1 13.2 + - - -
267H ARG 3.1 0.2 - - - -
268H ALA* 1.3 77.9 - - - +
270H GLN* 1.3 68.0 + - - +
272H ASN* 2.8 19.2 + - - +
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Residues in contact with GLN 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C HIS* 5.8 1.6 + - - -
440C GLY* 3.3 28.9 - - - +
441C ARG* 3.6 25.3 - - + +
445C VAL* 6.4 0.2 - - - +
449C GLN* 5.8 1.8 - - - +
266H GLU* 3.1 16.9 + - - +
267H ARG* 3.0 31.0 + - - +
269H SER* 1.3 78.1 - - - +
271H TYR* 1.3 79.1 + - + +
272H ASN* 3.3 4.0 + - - +
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Residues in contact with TYR 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C GLN 5.3 4.3 + - - -
440C GLY* 5.4 5.6 - - - -
336G SER* 2.8 31.2 + - - +
337G GLY* 5.9 0.3 - - - -
340G ILE* 3.1 14.7 - - - +
219H ALA 4.0 13.7 + - - -
220H SER 3.9 10.8 + - - -
222H PRO* 3.3 27.6 - - + -
228H CYS* 5.8 0.2 - - - -
267H ARG* 3.3 33.9 + - + +
268H ALA* 3.3 2.5 - - - +
270H GLN* 1.3 98.7 + - + +
272H ASN* 1.3 78.7 + - - +
273H ILE* 3.3 14.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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