Contacts of the helix formed by residues 302 - 317 (chain E) 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 PRO 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E GLU* 5.2 1.6 - - - +
293E ARG* 3.9 28.5 - - - +
300E GLN 3.3 6.0 - - - +
301E THR* 1.3 103.9 - - + +
303E SER* 1.3 70.6 + - - +
304E PHE* 3.3 5.1 + - + +
305E TRP* 3.4 25.3 + - + +
306E ILE* 3.4 6.6 + - - +
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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
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302E PRO* 1.3 75.0 - - - +
304E PHE* 1.3 68.8 + - - +
306E ILE* 3.2 14.4 + - - +
307E LEU* 3.4 15.2 + - - +
375E ILE* 4.0 21.9 - - - +
379E GLU* 3.5 23.5 + - - -
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Residues in contact with PHE 304 (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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170E PRO* 3.7 32.8 - - + -
171E VAL 4.3 5.6 - - - -
172E ILE* 4.0 21.8 - - + -
288E ILE* 4.4 13.5 - - + -
302E PRO* 3.3 4.9 + - + +
303E SER* 1.3 76.7 + - - +
305E TRP* 1.3 112.3 + + + +
307E LEU* 2.8 25.7 + - + +
308E ALA* 3.0 12.4 + - + +
383E LEU* 5.7 0.9 - - + -
390E LEU* 3.8 33.4 - - + -
392E VAL* 3.8 28.3 - - + -
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Residues in contact with TRP 305 (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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168E GLU* 3.1 24.6 + - - -
170E PRO* 5.3 1.2 - - + +
288E ILE* 3.2 36.3 - - + -
291E ASP* 3.9 12.6 - - + -
293E ARG* 3.4 34.7 - - + +
294E CYS* 3.6 30.4 - - + -
297E ILE* 6.4 0.7 - - - -
301E THR* 3.9 17.0 - - + -
302E PRO* 3.4 26.2 + - + +
304E PHE* 1.3 99.5 - + + +
306E ILE* 1.3 62.9 + - - +
308E ALA* 2.8 18.1 + - + +
309E ARG* 2.9 15.1 + - - +
392E VAL* 4.3 12.6 - - + -
394E ARG* 3.4 28.9 - - - -
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Residues in contact with ILE 306 (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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297E ILE* 4.2 10.8 - - + -
301E THR* 3.7 24.2 - - + +
302E PRO 3.4 4.7 + - - +
303E SER* 3.2 10.4 + - - +
304E PHE 3.1 0.8 - - - -
305E TRP* 1.3 75.6 - - - +
307E LEU* 1.3 56.8 + - - +
309E ARG* 3.0 8.3 + - - +
310E ALA* 2.6 35.6 + - + +
361E VAL* 4.4 10.5 - - + -
364E LEU* 3.7 17.2 - - + +
365E LEU* 3.6 29.4 - - + +
368E ILE* 4.2 18.8 - - + -
370E GLN* 4.3 12.6 - - - +
375E ILE* 4.1 18.8 - - + -
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Residues in contact with LEU 307 (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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172E ILE* 4.1 21.1 - - + -
303E SER* 3.7 21.1 - - - +
304E PHE* 2.8 13.1 + - + +
306E ILE* 1.3 75.9 - - - +
308E ALA* 1.3 55.5 + - - +
310E ALA* 3.4 6.2 - - - +
311E LEU* 2.9 31.2 + - - +
361E VAL* 3.8 22.2 - - + -
375E ILE* 3.9 25.4 - - + -
379E GLU* 4.6 14.8 - - + +
380E LEU* 4.6 5.4 - - + -
383E LEU* 3.0 39.6 - - + +
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Residues in contact with ALA 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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288E ILE* 4.2 13.9 - - + -
289E PHE* 3.4 8.3 - - + -
294E CYS* 4.1 9.0 - - - -
304E PHE* 3.0 12.7 + - + +
305E TRP* 2.8 37.6 + - + +
307E LEU* 1.3 73.9 - - - +
309E ARG* 1.3 67.6 + - - +
311E LEU* 2.9 21.3 + - - +
312E LYS 2.9 10.7 + - - -
383E LEU* 5.3 0.2 - - - +
390E LEU* 5.3 5.6 - - + -
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Residues in contact with ARG 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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294E CYS* 3.5 28.3 + - - +
295E ILE* 2.8 42.5 + - - +
297E ILE* 3.6 18.0 - - + +
305E TRP 2.9 9.1 + - - +
306E ILE 3.5 5.8 - - - +
308E ALA* 1.3 74.4 - - - +
310E ALA* 1.3 55.4 + - - +
311E LEU 2.7 10.9 + - - -
312E LYS* 2.8 20.8 + - - +
313E GLU* 2.8 53.3 + - + +
364E LEU* 3.2 28.0 - - + +
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Residues in contact with ALA 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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306E ILE 2.6 20.7 + - - +
307E LEU* 3.4 8.3 - - - +
309E ARG* 1.3 72.2 - - - +
311E LEU* 1.3 58.9 + - - +
313E GLU* 4.1 1.8 - - - -
314E PHE* 3.6 12.0 + - - +
357E VAL* 3.6 14.6 - - + +
360E HIS* 3.6 15.7 - - - +
361E VAL* 3.3 44.4 - - + +
364E LEU* 3.6 8.7 - - + +
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Residues in contact with LEU 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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289E PHE* 3.8 10.3 - - + -
307E LEU 2.9 7.8 + - - +
308E ALA* 2.9 10.9 + - - +
309E ARG 2.7 4.9 + - - -
310E ALA* 1.3 72.0 - - - +
312E LYS* 1.3 67.8 + - - +
313E GLU 3.1 1.3 - - - -
314E PHE* 2.7 15.0 + - + +
315E VAL* 2.8 14.6 + - - +
323E LEU* 4.2 17.7 - - + -
324E PRO* 4.0 13.2 - - + -
357E VAL* 3.3 35.4 - - + -
383E LEU* 3.7 32.8 - - + -
384E CYS* 4.8 2.7 - - - -
387E SER* 4.3 14.1 - - - -
390E LEU* 3.9 18.6 - - + -
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Residues in contact with LYS 312 (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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289E PHE* 3.3 57.8 + - + +
290E ASN* 4.9 5.8 + - - -
294E CYS* 4.4 3.1 - - - -
295E ILE* 3.7 30.7 - - - +
308E ALA 2.9 7.2 + - - +
309E ARG* 2.8 32.6 + - - +
311E LEU* 1.3 71.8 - - - +
313E GLU* 1.3 60.2 + - - +
315E VAL* 3.0 5.8 + - + +
316E ALA* 2.9 30.1 + - + +
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Residues in contact with GLU 313 (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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309E ARG* 2.8 57.9 + - + +
310E ALA* 4.8 1.3 - - - -
312E LYS* 1.3 77.8 - - - +
314E PHE* 1.3 56.8 + - - +
316E ALA* 3.8 9.5 - - - +
317E LYS* 3.0 31.4 + - - +
360E HIS* 3.8 27.6 + - + +
364E LEU* 4.9 10.1 - - + -
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Residues in contact with PHE 314 (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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310E ALA 3.6 12.1 + - - +
311E LEU* 2.7 16.9 + - - +
313E GLU* 1.3 71.1 - - - +
315E VAL* 1.3 63.4 + - - +
317E LYS 3.3 6.1 + - - -
318E GLU* 4.0 13.9 - - + -
319E GLY* 2.6 52.8 + - - -
322E ASN 3.6 12.8 - - - -
323E LEU* 3.7 1.3 - - - -
324E PRO* 3.6 24.7 - - + -
353E ASP* 3.0 40.8 - - + -
356E ALA* 3.3 32.5 - - + -
357E VAL* 3.4 21.3 - - + -
360E HIS* 3.7 11.2 - - + -
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Residues in contact with VAL 315 (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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281E ILE* 3.6 12.1 - - + -
289E PHE* 3.8 26.5 - - + -
311E LEU* 2.8 18.4 + - + +
312E LYS* 3.2 7.0 - - + +
314E PHE* 1.3 79.2 - - + +
316E ALA* 1.3 64.0 + - - +
320E GLN 3.4 3.5 + - - -
321E GLY* 2.9 57.8 + - - +
322E ASN 3.9 20.2 - - - +
323E LEU* 4.2 9.6 - - + +
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Residues in contact with ALA 316 (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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312E LYS* 2.9 16.3 + - + +
313E GLU* 3.8 11.9 - - - +
315E VAL* 1.3 80.5 - - - +
317E LYS* 1.3 63.5 + - + +
320E GLN* 4.8 1.2 + - - -
321E GLY 4.8 1.7 + - - -
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Residues in contact with LYS 317 (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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313E GLU* 3.0 14.1 + - - +
314E PHE 3.3 0.4 + - - -
316E ALA* 1.3 79.5 - - + +
318E GLU* 1.3 87.5 + - + +
319E GLY 2.7 17.7 + - - -
320E GLN* 2.9 15.6 + - - +
360E HIS* 3.8 10.5 - - + -
363E LYS* 4.0 20.2 - - - +
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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