Contacts of the helix formed by residues 260 - 275 (chain X) in PDB entry 3N5N
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 ARG 260 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X LEU* 4.0 30.7 - - + +
91X ASP* 2.9 42.8 + - - -
257X ASP* 3.1 17.0 + - - +
259X ALA* 1.3 88.7 - - + +
261X PRO* 1.3 61.1 - - - +
262X GLY 3.3 2.2 - - - -
263X ASP* 2.3 41.6 + - + +
264X PHE* 3.0 27.4 + - - +
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Residues in contact with PRO 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X SER* 3.9 4.0 - - - +
215X GLY* 3.2 36.6 - - - +
216X GLN 3.4 20.4 - - - +
217X ALA* 3.8 11.4 - - - -
256X VAL* 3.8 14.7 - - + +
257X ASP 3.0 17.2 - - - +
258X PRO 4.0 3.1 - - - +
259X ALA 3.5 7.9 - - - +
260X ARG* 1.3 89.9 - - - +
262X GLY* 1.3 65.4 + - - +
264X PHE* 3.3 1.6 + - + +
265X ASN* 3.0 29.8 + - - -
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Residues in contact with GLY 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211X SER* 3.2 32.2 + - - -
212X ILE* 4.0 9.2 - - - -
260X ARG* 3.3 0.6 - - - +
261X PRO* 1.3 81.1 - - - +
263X ASP* 1.3 63.3 + - - +
265X ASN* 3.2 3.8 + - - +
266X GLN* 3.0 31.2 + - - +
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Residues in contact with ASP 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X LEU* 3.6 10.5 - - + -
90X TYR* 4.0 23.3 + - + -
91X ASP* 4.4 0.2 - - - +
94X LYS* 5.7 2.7 + - - -
260X ARG* 2.3 50.4 + - + +
261X PRO 3.4 0.4 - - - -
262X GLY* 1.3 76.3 - - - +
264X PHE* 1.3 53.7 + - - +
266X GLN* 3.6 7.9 - - - +
267X ALA* 2.7 37.6 + - - +
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Residues in contact with PHE 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X PHE* 4.1 16.4 - + - -
83X ARG* 4.1 17.5 - - + -
86X LEU* 3.8 24.3 - - + +
87X LEU* 3.8 12.5 - - + +
252X ALA* 4.8 5.2 - - + -
255X LEU* 3.5 35.2 - - + -
256X VAL* 3.6 26.5 - - + -
257X ASP* 3.7 24.7 - - + +
260X ARG 3.0 18.5 + - - +
261X PRO 3.7 3.8 - - - +
262X GLY 3.1 0.2 - - - -
263X ASP* 1.3 77.4 - - - +
265X ASN* 1.3 65.0 + - - +
267X ALA* 3.1 3.4 + - - +
268X ALA* 2.9 36.1 + - + +
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Residues in contact with ASN 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X GLY 4.3 0.2 + - - -
208X ALA* 5.4 2.0 - - - +
211X SER* 2.8 31.3 + - - +
212X ILE* 5.6 2.7 - - + -
218X THR 3.0 19.8 + - - -
219X GLY* 3.6 6.8 - - - -
220X VAL* 3.3 41.1 + - + +
225X VAL* 4.7 2.1 - - - +
256X VAL* 3.8 6.3 - - - +
261X PRO 3.0 14.6 + - - +
262X GLY 3.7 3.8 - - - +
264X PHE* 1.3 82.7 - - - +
266X GLN* 1.3 63.7 + - + +
268X ALA* 3.3 6.6 + - - +
269X MET* 3.1 24.1 + - - +
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Residues in contact with GLN 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X TYR* 3.5 17.3 + - + +
99X TRP* 5.0 4.8 - - - +
100X ARG* 2.5 55.2 + - - +
103X ALA* 5.9 1.0 - - - +
212X ILE* 3.7 40.1 - - + +
262X GLY 3.0 21.8 + - - +
263X ASP* 3.9 8.4 - - - +
265X ASN* 1.3 76.3 - - + +
267X ALA* 1.3 57.9 + - - +
269X MET* 3.9 5.0 - - - +
270X GLU* 2.9 30.1 + - - +
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Residues in contact with ALA 267 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X LEU* 3.7 25.3 - - + +
87X LEU* 4.6 2.2 - - + -
89X TRP* 3.8 1.0 - - - -
90X TYR* 3.4 37.4 - - + -
263X ASP 2.7 22.4 + - - +
264X PHE* 3.5 6.1 - - - +
266X GLN* 1.3 71.7 - - - +
268X ALA* 1.3 61.1 + - - +
270X GLU* 3.5 1.6 - - - +
271X LEU* 2.9 31.0 + - - +
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Residues in contact with ALA 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82X PHE* 6.0 1.3 - - + -
86X LEU* 3.7 14.7 - - + +
225X VAL* 3.6 27.6 - - + +
228X VAL* 4.1 12.2 - - + +
264X PHE* 2.9 28.6 + - + +
265X ASN* 3.7 4.0 - - - +
267X ALA* 1.3 77.8 - - - +
269X MET* 1.3 61.9 + - - +
271X LEU* 3.4 6.6 + - - +
272X GLY* 3.2 16.6 + - - -
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Residues in contact with MET 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204X TYR* 5.3 5.6 - - - +
222X ASP* 4.2 18.4 - - - +
224X ASN* 3.6 13.5 - - + +
225X VAL* 3.7 11.8 - - + +
265X ASN 3.1 15.4 + - - +
266X GLN* 3.9 5.8 - - - +
268X ALA* 1.3 77.3 - - - +
270X GLU* 1.3 57.4 + - - +
272X GLY* 2.9 4.5 + - - -
273X ALA* 2.9 27.7 + - - +
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Residues in contact with GLU 270 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X TRP* 3.6 18.8 - - + -
90X TYR* 4.2 7.4 - - + -
93X GLU 4.2 1.0 - - - +
94X LYS* 3.2 6.6 - - - -
95X ARG* 2.6 67.3 + - - +
100X ARG* 2.9 24.3 + - - -
266X GLN 2.9 19.7 + - - +
267X ALA* 3.2 8.0 + - - +
269X MET* 1.3 72.6 - - - +
271X LEU* 1.3 56.3 + - - +
273X ALA* 3.6 5.4 - - - +
274X THR* 2.4 46.3 + - + +
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Residues in contact with LEU 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X PHE* 6.0 0.9 - - + -
86X LEU* 4.1 16.2 - - + -
89X TRP* 3.7 13.0 - - + -
228X VAL* 3.9 30.3 - - + -
267X ALA 2.9 17.2 + - - +
268X ALA* 3.5 7.0 - - - +
269X MET 3.2 0.2 - - - -
270X GLU* 1.3 75.9 - - - +
272X GLY* 1.3 53.2 + - - +
274X THR* 3.9 0.4 - - - -
275X VAL* 2.9 39.9 + - + -
276X CYS* 2.7 34.0 + - + -
286X CYS* 4.2 16.6 - - - -
287X PRO* 3.7 25.8 - - + -
288X VAL* 4.9 7.6 - - + -
400X SF4 4.4 6.5 - - - -
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Residues in contact with GLY 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224X ASN* 3.5 19.5 - - - -
227X ARG* 2.9 17.8 + - - -
228X VAL* 3.8 18.1 - - - +
268X ALA 3.2 4.2 + - - -
269X MET 2.9 8.4 + - - -
271X LEU* 1.3 81.9 - - - +
273X ALA* 1.3 58.2 + - - +
276X CYS 3.2 18.0 - - - +
277X THR* 3.8 3.5 - - - +
278X PRO* 4.7 0.5 - - - +
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Residues in contact with ALA 273 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X ARG* 4.0 27.8 + - - +
224X ASN* 3.7 15.7 + - - +
227X ARG* 4.8 0.2 - - - +
269X MET 2.9 14.8 + - - +
270X GLU* 3.1 4.5 + - - +
272X GLY* 1.3 78.8 - - - +
274X THR* 1.3 62.0 + - - +
277X THR* 3.9 9.5 - - - +
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Residues in contact with THR 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X TRP* 3.6 17.2 - - - -
93X GLU 6.1 0.4 - - - +
95X ARG* 3.9 35.2 - - + +
270X GLU* 2.4 30.8 + - + +
273X ALA* 1.3 82.8 - - - +
275X VAL* 1.3 67.9 + - - +
277X THR* 3.3 16.1 - - - +
282X LEU* 4.1 13.1 - - - +
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Residues in contact with VAL 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X TRP* 3.7 35.0 - - + +
271X LEU* 2.9 21.3 + - + -
274X THR* 1.3 74.4 + - - +
276X CYS* 1.3 57.5 + - - +
277X THR 3.1 9.7 + - - -
281X PRO* 3.3 0.9 - - - +
282X LEU* 2.8 70.3 + - + +
285X GLN* 4.5 7.2 - - + +
286X CYS* 3.8 22.9 - - + +
400X SF4 3.9 3.6 - - - -
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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