Contacts of the helix formed by residues 277 - 290 (chain E) in PDB entry 2P1N
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 VAL 277 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245E TYR* 3.1 12.8 + - - +
246E THR* 3.8 19.5 - - - +
247E ALA 4.8 6.3 - - - +
249E VAL* 5.3 4.7 - - + -
275E ASP 3.6 13.0 - - - +
276E ALA* 1.3 73.7 - - - +
278E PRO* 1.4 72.3 - - + +
279E ALA* 2.6 12.8 + - + +
280E TYR* 2.9 46.3 + - + +
281E LEU* 3.7 8.0 + - - +
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Residues in contact with PRO 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E ALA 3.9 2.7 - - - +
277E VAL* 1.4 83.4 - - + -
279E ALA* 1.3 60.4 + - - +
280E TYR 3.3 1.0 + - - -
281E LEU* 3.4 26.1 + - + +
282E PRO* 3.6 9.0 - - - +
301E VAL* 3.8 17.0 - - + -
305E ASP* 3.7 33.0 - - - +
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Residues in contact with ALA 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E VAL* 4.3 32.5 - - + +
254E TYR* 3.8 14.9 - - - -
277E VAL* 2.6 12.5 + - + +
278E PRO* 1.3 75.6 - - - +
280E TYR* 1.3 58.9 + - + +
281E LEU 3.7 0.2 - - - -
282E PRO* 3.8 10.2 - - - +
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Residues in contact with TYR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU* 3.9 18.4 - - + -
245E TYR* 2.8 32.3 + - + -
247E ALA* 3.7 16.6 - - + -
248E GLU 2.9 28.4 + - - -
249E VAL* 3.8 12.1 - - + -
250E ARG 2.9 17.2 + - - -
253E VAL* 3.2 35.6 - - + +
254E TYR* 3.7 32.3 - + + -
257E LEU* 4.1 9.2 - - + -
277E VAL* 2.9 30.3 + - + +
279E ALA* 1.3 83.4 - - + +
281E LEU* 1.3 58.2 + - - -
282E PRO* 3.1 7.2 - - - -
283E ALA* 3.5 12.9 + - - +
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Residues in contact with LEU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E TYR* 3.8 11.4 - - + -
273E PHE* 3.8 35.2 - - + -
276E ALA* 5.1 5.2 - - + -
277E VAL 3.7 3.5 + - - +
278E PRO* 3.4 17.8 + - + +
280E TYR* 1.3 70.3 - - - +
282E PRO* 1.3 66.9 - - + +
283E ALA 3.0 6.3 - - - -
284E VAL* 2.8 28.2 + - + +
285E TYR* 3.6 12.1 - - + +
296E LEU* 4.8 4.0 - - + -
301E VAL* 3.9 34.8 - - + -
305E ASP* 4.8 13.2 - - + +
309E LEU* 4.4 21.3 - - + -
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Residues in contact with PRO 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 3.2 16.5 + - + +
258E SER* 5.4 0.3 + - - -
278E PRO 3.6 13.5 - - - +
279E ALA* 3.8 11.0 - - - +
280E TYR 3.1 6.5 - - - -
281E LEU* 1.3 93.6 - - + +
283E ALA* 1.3 54.8 + - - +
284E VAL 2.9 1.3 - - - -
285E TYR* 2.8 64.3 + - + +
286E SER 4.7 0.5 + - - -
308E LYS* 5.8 3.8 - - - -
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E TYR* 4.2 1.8 - - - +
254E TYR* 3.0 25.5 + - + -
257E LEU* 3.8 30.1 - - + -
258E SER* 4.4 18.2 + - - +
261E LEU* 3.4 23.7 - - + +
280E TYR 3.5 14.7 + - - +
281E LEU 3.0 0.2 - - - -
282E PRO* 1.3 78.1 - - - +
284E VAL* 1.3 59.7 + - - +
285E TYR 3.2 1.6 + - - -
286E SER* 4.6 5.4 + - - -
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Residues in contact with VAL 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E THR* 5.9 1.8 - - + -
245E TYR* 3.6 20.2 - - + +
261E LEU* 3.8 19.5 - - + -
270E LEU* 3.4 35.2 - - + -
273E PHE* 4.1 16.8 - - + -
281E LEU* 2.8 11.0 + - + +
283E ALA* 1.3 79.1 - - - +
285E TYR* 1.4 61.5 + - - +
287E VAL* 3.6 12.9 + - - +
288E CYS* 3.2 25.2 + - - +
294E LEU* 5.8 0.4 - - + -
309E LEU* 3.7 15.5 - - + -
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Residues in contact with TYR 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E LEU* 3.6 10.7 - - + +
282E PRO* 2.8 52.7 + - + +
283E ALA 3.2 1.2 - - - -
284E VAL* 1.4 74.7 - - - +
286E SER* 1.3 69.4 + - - +
287E VAL 2.9 2.5 - - - -
288E CYS* 2.7 23.3 + - + +
289E SER* 4.1 3.6 + - - -
305E ASP 4.9 1.7 + - - -
308E LYS* 3.6 40.6 - - + +
309E LEU* 4.0 30.6 + - + -
312E GLN* 3.4 38.8 - - + +
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Residues in contact with SER 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E SER* 4.9 2.0 + - - -
261E LEU 4.4 0.5 - - - -
262E SER* 3.0 40.3 + - - -
282E PRO 4.7 0.4 + - - -
283E ALA 4.6 5.6 + - - -
284E VAL 3.9 0.2 - - - -
285E TYR* 1.3 74.6 - - - +
287E VAL* 1.3 64.6 + - - +
288E CYS 3.2 1.0 + - - -
289E SER* 3.5 13.6 + - - -
290E ARG* 3.8 16.2 + - - -
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Residues in contact with VAL 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LEU* 3.1 37.2 - - + +
264E CYS 3.5 20.0 - - - +
267E LEU* 3.8 30.9 - - + +
270E LEU* 4.9 7.6 - - + -
284E VAL* 3.6 9.7 + - - +
285E TYR 2.7 3.8 + - - -
286E SER* 1.3 77.9 + - - +
288E CYS* 1.3 58.3 + - - +
289E SER 3.3 2.9 - - - -
290E ARG* 3.4 31.1 + - - +
291E LEU* 3.5 24.3 + - + +
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Residues in contact with CYS 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E VAL* 3.2 20.4 - - - -
285E TYR* 2.7 17.5 + - - +
287E VAL* 1.3 75.8 - - - +
289E SER* 1.3 59.2 + - - +
290E ARG 3.2 2.0 + - - -
291E LEU* 3.6 26.0 + - - -
294E LEU* 5.5 0.9 - - - -
309E LEU* 3.4 30.7 - - - -
312E GLN* 2.2 34.3 - - + +
313E CYS* 3.1 25.2 - - - +
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Residues in contact with SER 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E TYR 4.4 1.7 + - - -
286E SER* 3.5 14.3 + - - -
287E VAL 3.3 0.4 - - - -
288E CYS* 1.3 80.5 + - - +
290E ARG* 1.3 64.7 + - - +
291E LEU 3.7 0.2 - - - -
312E GLN* 3.7 8.3 + - - +
314E PRO* 4.1 11.7 - - - +
315E LYS* 3.5 24.0 + - - +
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Residues in contact with ARG 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E SER 4.0 15.6 + - - -
264E CYS 3.8 9.5 + - - -
265E LYS* 3.8 39.8 + - - +
267E LEU 4.1 3.7 + - - +
268E ARG* 3.3 36.1 - - - +
286E SER* 3.8 16.5 + - - -
287E VAL* 3.4 37.1 + - - +
288E CYS 3.2 0.2 - - - -
289E SER* 1.3 90.5 - - - +
291E LEU* 1.3 66.1 + - - +
292E THR* 3.3 6.8 + - - +
315E LYS* 4.5 12.2 - - - +
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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