Contacts of the helix formed by residues 302 - 317 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A GLU* 5.2 1.6 - - - +
293A ARG* 3.9 27.6 - - - +
300A GLN 3.2 6.0 - - - +
301A THR* 1.3 103.4 - - + +
303A SER* 1.3 68.4 + - - +
304A PHE* 3.2 6.2 + - + +
305A TRP* 3.4 30.1 + - + +
306A ILE* 3.4 3.8 + - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A PRO* 1.3 74.0 - - - +
304A PHE* 1.3 68.1 + - - +
306A ILE* 3.2 15.2 + - - +
307A LEU* 3.4 14.6 + - - +
375A ILE* 4.0 22.6 - - - +
379A GLU* 3.5 22.8 + - - -
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PRO* 3.6 34.3 - - + -
171A VAL 4.3 6.5 - - - -
172A ILE* 3.9 22.0 - - + -
288A ILE* 4.4 11.4 - - + -
302A PRO* 3.3 4.8 - - + +
303A SER* 1.3 77.2 - - - +
305A TRP* 1.3 104.9 + + + +
307A LEU* 2.8 33.0 + - + +
308A ALA* 3.0 12.4 + - + -
383A LEU* 5.7 1.3 - - + -
390A LEU* 3.7 35.4 - - + -
391A ARG 5.2 0.2 - - - -
392A VAL* 3.8 30.1 - - + -
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 3.1 25.9 + - - -
170A PRO* 5.3 1.5 - - + +
288A ILE* 3.2 43.7 - - + -
291A ASP* 3.9 12.8 - - + -
293A ARG* 3.4 34.6 - - + +
294A CYS* 3.6 22.8 - - + -
297A ILE* 6.4 0.4 - - - -
301A THR* 3.9 17.0 - - + -
302A PRO* 3.4 25.8 + - + +
304A PHE* 1.3 99.1 - + + +
306A ILE* 1.3 63.2 + - - +
308A ALA* 2.9 18.6 + - + +
309A ARG* 2.9 14.7 + - - +
392A VAL* 4.2 12.8 - - + -
394A ARG* 3.3 28.9 - - - -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ILE* 4.2 10.5 - - + -
301A THR* 3.7 25.4 - - + +
302A PRO 3.4 3.7 + - - +
303A SER* 3.2 9.7 + - - +
304A PHE 3.0 0.8 + - - -
305A TRP* 1.3 76.7 - - - +
307A LEU* 1.3 55.3 + - - +
309A ARG* 3.0 8.2 + - - +
310A ALA* 2.6 36.7 + - + +
361A VAL* 4.4 10.5 - - + -
364A LEU* 3.7 16.6 - - + +
365A LEU* 3.6 29.8 - - + +
368A ILE* 4.2 19.5 - - + -
370A GLN* 4.3 10.8 - - - +
375A ILE* 4.2 17.3 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.1 22.0 - - + -
303A SER* 3.6 20.6 - - - +
304A PHE* 2.8 16.9 + - - +
306A ILE* 1.3 73.2 - - - +
308A ALA* 1.3 60.9 + - - +
310A ALA* 3.4 6.5 - - - +
311A LEU* 2.9 25.6 + - - +
361A VAL* 3.7 23.6 - - + -
375A ILE* 3.8 25.6 - - + -
379A GLU* 4.6 14.6 - - + +
380A LEU* 4.6 4.7 - - + -
383A LEU* 3.0 40.3 - - + +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ILE* 4.1 14.1 - - + -
289A PHE* 3.4 8.1 - - + -
294A CYS* 4.1 9.6 - - - -
304A PHE* 3.0 13.1 + - + +
305A TRP* 2.9 35.4 + - + +
307A LEU* 1.3 73.5 - - - +
309A ARG* 1.3 66.6 + - - +
311A LEU* 2.9 21.9 + - - +
312A LYS 2.9 10.7 + - - -
383A LEU* 5.3 0.2 - - - +
390A LEU* 5.3 5.4 - - + -
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A CYS* 3.4 27.4 + - - +
295A ILE* 2.8 42.0 + - - +
297A ILE* 3.6 17.8 - - + +
305A TRP 2.9 9.3 + - - +
306A ILE 3.5 5.8 - - - +
308A ALA* 1.3 70.6 - - - +
310A ALA* 1.3 55.4 + - - +
311A LEU 2.7 15.7 + - - -
312A LYS* 2.8 19.7 + - - +
313A GLU* 2.7 55.2 + - + +
364A LEU* 3.2 27.8 - - + +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE 2.6 21.4 + - - +
307A LEU* 3.4 7.6 - - - +
309A ARG* 1.3 73.5 - - - +
311A LEU* 1.3 58.4 + - - +
313A GLU* 4.1 1.1 - - - -
314A PHE* 3.5 13.0 + - - +
357A VAL* 3.6 13.7 - - + +
360A HIS* 3.6 16.7 - - - +
361A VAL* 3.3 44.2 - - + +
364A LEU* 3.9 8.5 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A PHE* 3.8 10.5 - - + -
307A LEU 2.9 8.0 + - - +
308A ALA* 2.9 10.9 + - - +
309A ARG 2.7 0.8 + - - -
310A ALA* 1.3 75.6 - - - +
312A LYS* 1.3 66.6 + - - +
313A GLU 3.1 1.3 - - - -
314A PHE* 2.8 15.2 + - - +
315A VAL* 2.8 14.6 + - - +
323A LEU* 4.1 18.2 - - + -
324A PRO* 4.0 13.0 - - + -
357A VAL* 3.3 35.7 - - + -
383A LEU* 3.8 31.9 - - + -
384A CYS* 4.8 2.7 - - - -
387A SER* 4.3 13.9 - - - -
390A LEU* 3.9 19.3 - - + -
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A PHE* 3.3 58.0 + - + +
290A ASN* 5.0 5.6 + - - -
294A CYS* 4.4 6.5 - - - -
295A ILE* 3.7 30.9 - - - +
308A ALA 2.9 6.6 + - - +
309A ARG* 2.8 24.3 + - - +
311A LEU* 1.3 76.2 - - - +
313A GLU* 1.3 59.0 + - - +
315A VAL* 3.0 5.8 + - + +
316A ALA* 2.9 30.3 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ARG* 2.7 58.7 + - + +
310A ALA* 4.1 2.5 - - - +
312A LYS* 1.3 77.3 - - - +
314A PHE* 1.3 56.8 + - - +
316A ALA* 3.6 9.6 + - - +
317A LYS* 3.0 31.5 + - - +
360A HIS* 3.8 27.4 + - + +
364A LEU* 4.8 10.3 - - + -
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ALA 3.5 11.7 + - - +
311A LEU* 2.8 11.8 + - - +
313A GLU* 1.3 76.7 - - - +
315A VAL* 1.3 62.0 + - - +
317A LYS 3.4 5.2 + - - -
318A GLU* 4.0 14.4 - - + -
319A GLY* 2.6 53.7 + - - -
322A ASN 3.6 13.0 - - - -
323A LEU* 3.8 0.9 - - - -
324A PRO* 3.7 24.9 - - + -
353A ASP* 3.0 39.0 - - + -
356A ALA* 3.3 32.3 - - + -
357A VAL* 3.4 22.7 - - + -
360A HIS* 3.7 11.4 - - + -
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE* 3.6 12.1 - - + -
289A PHE* 3.8 26.9 - - + -
311A LEU 2.8 18.8 + - - +
312A LYS* 3.0 6.9 + - + +
314A PHE* 1.3 79.8 - - + +
316A ALA* 1.3 64.3 + - - +
320A GLN 3.4 2.9 + - - -
321A GLY* 2.9 58.8 + - - +
322A ASN 4.0 20.9 - - - +
323A LEU* 4.2 9.4 - - + +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 2.9 15.9 + - + +
313A GLU* 3.8 12.3 - - - +
315A VAL* 1.3 81.5 - - - +
317A LYS* 1.3 63.8 + - + +
320A GLN* 4.8 1.4 + - - -
321A GLY* 4.8 2.1 + - - -
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU 3.0 14.4 + - - +
314A PHE 3.4 0.2 - - - -
316A ALA* 1.3 81.5 - - + +
318A GLU* 1.3 89.3 + - + +
319A GLY 2.7 17.4 + - - -
320A GLN* 2.9 15.4 + - - +
360A HIS* 3.8 10.1 - - + -
363A LYS* 4.0 20.6 - - - +
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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