Contacts of the helix formed by residues 302 - 311 (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 GLN 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278E PRO* 5.9 0.2 - - - +
300E THR 4.8 3.6 + - - +
301E VAL* 1.3 77.8 - - - +
303E SER* 1.3 76.3 + - - +
304E TYR* 3.2 4.0 - - + +
305E ASP* 2.7 27.8 + - - +
306E LEU* 3.1 9.2 + - - -
324E TYR* 4.0 32.2 - - - +
326E GLU* 5.4 4.2 - - - +
357E VAL* 5.5 1.3 - - - +
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Residues in contact with SER 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E GLN* 1.3 77.3 + - - +
304E TYR* 1.3 59.4 + - - +
306E LEU* 2.9 12.9 + - - +
307E VAL* 2.7 30.4 + - - +
324E TYR 3.6 20.9 + - - -
325E ILE* 4.4 0.9 - - - +
326E GLU* 3.9 24.0 + - - +
328E ALA* 5.3 2.8 - - - +
329E GLY* 3.9 24.1 + - - -
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Residues in contact with TYR 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E GLN* 3.0 4.7 + - + +
303E SER* 1.3 77.5 - - - +
305E ASP* 1.3 63.8 + - - +
307E VAL* 3.6 16.7 - - + +
308E LYS* 3.0 62.9 + - + +
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Residues in contact with ASP 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E PRO* 3.7 35.2 - - - +
281E LEU* 4.8 11.1 - - + +
285E TYR* 4.9 1.9 + - - -
301E VAL* 4.1 15.0 - - + -
302E GLN* 2.7 33.9 + - - +
304E TYR* 1.3 73.7 - - - +
306E LEU* 1.3 65.5 + - - +
308E LYS* 3.4 32.8 + - - +
309E LEU* 3.5 11.1 + - - +
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Residues in contact with LEU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E LEU* 3.9 32.1 - - + -
299E ALA* 5.4 1.1 - - + -
301E VAL* 3.6 32.5 - - + +
302E GLN 3.1 5.1 + - - +
303E SER* 2.9 9.7 + - - +
305E ASP* 1.3 76.2 - - - +
307E VAL* 1.3 54.9 + - - +
309E LEU* 2.7 30.5 + - + +
310E LEU* 2.8 21.7 + - + +
321E VAL* 4.1 11.4 - - + -
322E LEU* 4.6 2.5 - - + +
324E TYR* 4.0 4.9 - - + -
325E ILE* 3.2 53.2 - - + +
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Residues in contact with VAL 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E SER* 2.7 22.7 + - - +
304E TYR* 3.6 20.6 - - + +
306E LEU* 1.3 71.4 - - + +
308E LYS* 1.3 68.5 + - + +
309E LEU 2.8 1.4 + - - -
310E LEU* 3.0 8.8 + - + +
311E CYS* 3.0 33.2 + - - -
328E ALA 5.1 0.2 - - - -
329E GLY* 3.7 30.3 - - - +
332E VAL* 3.9 27.8 - - + -
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Residues in contact with LYS 308 (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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282E PRO* 5.8 3.4 - - - -
285E TYR* 3.6 26.5 - - + +
304E TYR* 3.0 55.4 + - + +
305E ASP* 3.6 27.8 + - - +
306E LEU 3.2 0.6 - - - -
307E VAL* 1.3 78.2 - - + +
309E LEU* 1.3 61.4 + - - +
311E CYS* 4.0 11.6 - - - +
312E GLN* 3.9 18.0 + - - -
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Residues in contact with LEU 309 (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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273E PHE* 5.5 0.4 - - + -
281E LEU* 4.4 19.3 - - + +
284E VAL* 3.7 16.4 - - + -
285E TYR* 4.0 21.1 - - + -
288E CYS* 3.4 32.8 - - - -
294E LEU* 4.2 12.1 - - + -
296E LEU* 3.7 40.6 - - + -
305E ASP 3.5 8.4 + - - +
306E LEU* 2.7 14.0 + - + +
308E LYS* 1.3 77.4 - - - +
310E LEU* 1.3 69.7 + - + +
312E GLN* 2.9 17.0 + - - +
313E CYS* 3.3 15.0 - - - -
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Residues in contact with LEU 310 (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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294E LEU* 3.6 29.6 - - + -
296E LEU* 4.8 4.3 - - + -
306E LEU* 2.8 26.7 + - + +
307E VAL* 3.7 8.3 - - - +
309E LEU* 1.3 74.6 - - + +
311E CYS* 1.3 53.8 + - - +
312E GLN 2.5 17.8 + - - -
313E CYS* 2.9 20.6 + - - +
316E LEU* 4.2 10.1 - - + -
319E LEU* 3.9 29.8 - - + -
321E VAL* 5.3 2.0 - - + -
325E ILE* 4.4 23.3 - - + -
329E GLY 5.1 2.9 - - - +
332E VAL* 5.4 7.0 - - + -
333E LEU* 4.3 18.4 - - + -
336E THR* 4.6 8.1 + - - +
337E CYS* 4.7 3.3 - - - -
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Residues in contact with CYS 311 (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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307E VAL* 3.0 26.7 + - - +
308E LYS* 4.0 10.3 - - - +
309E LEU 3.2 0.2 - - - -
310E LEU* 1.3 73.9 - - - +
312E GLN* 1.3 60.9 + - + +
313E CYS 3.4 1.5 + - - -
314E PRO* 5.1 4.7 - - - +
332E VAL* 3.9 22.9 - - - -
336E THR* 4.5 23.6 + - + +
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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