Contacts of the helix formed by residues 302 - 317 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C GLU* 5.1 1.6 - - - +
293C ARG* 3.9 27.8 - - - +
300C GLN 3.2 6.2 - - - +
301C THR* 1.3 104.5 - - + +
303C SER* 1.3 69.1 + - - +
304C PHE* 3.3 5.9 + - + +
305C TRP* 3.4 29.6 + - + +
306C ILE* 3.4 2.8 + - - +
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Residues in contact with SER 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C PRO* 1.3 74.5 - - - +
304C PHE* 1.3 68.7 + - - +
306C ILE* 3.2 14.4 + - - +
307C LEU* 3.4 14.5 + - - +
375C ILE* 4.0 22.8 - - - +
379C GLU* 3.5 23.3 + - - -
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Residues in contact with PHE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PRO* 3.6 33.4 - - + -
171C VAL 4.4 6.3 - - - -
172C ILE* 4.0 20.4 - - + -
288C ILE* 4.4 11.9 - - + -
302C PRO* 3.3 4.8 + - + +
303C SER* 1.3 76.9 + - - +
305C TRP* 1.3 99.1 - + + +
307C LEU* 2.8 37.8 + - + +
308C ALA* 3.0 11.1 + - + -
383C LEU* 5.7 0.9 - - + -
390C LEU* 3.8 35.7 - - + -
391C ARG 5.2 0.2 - - - -
392C VAL* 3.9 30.1 - - + -
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Residues in contact with TRP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C GLU* 3.0 24.6 + - - -
170C PRO* 5.4 1.1 - - + +
288C ILE* 3.2 35.9 - - + -
291C ASP* 3.9 12.6 - - + -
293C ARG* 3.3 36.5 - - + +
294C CYS* 3.6 30.6 - - + -
297C ILE* 6.5 0.4 - - - -
301C THR* 3.9 16.4 - - + -
302C PRO* 3.4 25.4 + - + +
304C PHE* 1.3 96.6 - + + +
306C ILE* 1.3 63.3 - - - +
308C ALA* 2.9 10.0 + - + +
309C ARG* 2.9 22.2 + - - +
392C VAL* 4.2 12.8 - - + -
394C ARG* 3.3 28.9 - - - -
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ILE* 4.2 10.8 - - + -
301C THR* 3.7 24.5 - - + +
302C PRO 3.4 4.5 + - - +
303C SER* 3.2 10.0 + - - +
304C PHE 3.0 1.0 + - - -
305C TRP* 1.3 77.0 - - - +
307C LEU* 1.3 56.4 + - - +
309C ARG* 3.0 8.1 + - - +
310C ALA* 2.6 36.5 + - + +
361C VAL* 4.4 9.9 - - + -
364C LEU* 3.7 17.7 - - + +
365C LEU* 3.6 35.9 - - + +
368C ILE* 4.2 20.4 - - + -
370C GLN* 4.3 11.0 - - - +
375C ILE* 4.2 12.1 - - + -
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 4.1 20.9 - - + -
303C SER* 3.7 21.8 - - - +
304C PHE* 2.8 15.8 + - + +
306C ILE* 1.3 73.0 - - - +
308C ALA* 1.3 61.1 + - - +
310C ALA* 3.3 6.2 + - - +
311C LEU* 2.9 25.8 + - - +
361C VAL* 3.7 23.3 - - + -
375C ILE* 3.8 24.5 - - + -
379C GLU* 4.6 15.5 - - + +
380C LEU* 4.6 5.4 - - + -
383C LEU* 3.0 41.0 - - + +
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ILE* 4.2 13.9 - - + -
289C PHE* 3.4 7.6 - - + -
294C CYS* 4.1 10.5 - - - -
304C PHE* 3.0 13.3 + - + +
305C TRP* 2.9 36.4 + - + +
307C LEU* 1.3 74.0 - - - +
309C ARG* 1.3 67.0 + - - +
311C LEU* 2.8 20.9 + - - +
312C LYS 2.9 10.7 + - - -
383C LEU* 5.3 0.2 - - - +
390C LEU* 5.3 5.4 - - + -
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Residues in contact with ARG 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C CYS* 3.4 27.6 + - - +
295C ILE* 2.8 42.3 + - - +
297C ILE* 3.6 18.8 - - + +
305C TRP 2.9 9.8 + - - +
306C ILE 3.5 5.4 - - - +
308C ALA* 1.3 74.0 - - - +
310C ALA* 1.3 55.3 + - - +
311C LEU 2.6 11.8 + - - -
312C LYS* 2.7 30.8 + - - +
313C GLU* 2.8 45.8 + - + +
364C LEU* 3.2 27.6 - - + +
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ILE 2.6 21.4 + - - +
307C LEU* 3.4 7.6 - - - +
309C ARG* 1.3 72.2 - - - +
311C LEU* 1.3 60.0 + - - +
313C GLU* 4.1 1.3 - - - -
314C PHE* 3.5 12.6 + - - +
357C VAL* 3.6 11.9 - - + +
360C HIS* 3.6 17.4 - - - +
361C VAL* 3.3 44.9 - - + +
364C LEU* 3.9 8.5 - - + -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ILE* 6.2 0.2 - - + -
289C PHE* 3.8 11.2 - - + -
307C LEU 2.9 7.3 + - - +
308C ALA* 2.8 11.2 + - - +
309C ARG 2.6 4.6 + - - -
310C ALA* 1.3 73.2 - - - +
312C LYS* 1.3 65.8 + - - +
313C GLU 3.1 1.1 - - - -
314C PHE* 2.7 15.7 + - - +
315C VAL* 2.8 14.6 + - - +
323C LEU* 4.1 17.5 - - + -
324C PRO* 4.0 13.7 - - + -
357C VAL* 3.3 35.2 - - + -
383C LEU* 3.8 30.7 - - + -
384C CYS* 4.9 2.7 - - - -
387C SER* 4.3 14.8 - - - -
390C LEU* 3.9 19.1 - - + -
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Residues in contact with LYS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C PHE* 3.3 58.3 + - + +
290C ASN* 4.9 6.3 + - - -
294C CYS* 4.4 6.1 - - - -
295C ILE* 3.7 31.5 - - - +
308C ALA 2.9 6.7 + - - +
309C ARG* 2.7 29.1 + - - +
311C LEU* 1.3 72.0 - - - +
313C GLU* 1.3 60.9 + - - +
315C VAL* 2.9 6.0 + - + +
316C ALA* 2.9 29.5 + - + +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C ARG* 2.8 58.1 + - + +
310C ALA* 4.1 2.5 - - - +
312C LYS* 1.3 78.1 - - - +
314C PHE* 1.3 57.5 + - - +
316C ALA* 3.6 8.9 + - - +
317C LYS* 3.0 31.4 + - - +
360C HIS* 3.9 26.0 + - + +
364C LEU* 4.8 10.8 - - + -
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Residues in contact with PHE 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ALA 3.5 11.7 + - - +
311C LEU 2.7 17.0 + - - +
313C GLU* 1.3 71.1 - - - +
315C VAL* 1.3 60.6 + - - +
317C LYS 3.3 6.2 + - - -
318C GLU* 3.6 14.1 + - + -
319C GLY* 2.6 52.4 + - - -
322C ASN 3.6 12.8 - - - -
323C LEU* 3.8 1.1 - - - -
324C PRO* 3.6 25.8 - - + -
353C ASP* 3.0 39.9 - - + -
356C ALA* 3.2 35.2 - - + -
357C VAL* 3.5 18.4 - - + -
360C HIS* 3.7 11.6 - - + -
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Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 3.6 11.0 - - + -
289C PHE* 3.8 26.7 - - + -
311C LEU* 2.8 17.9 + - + +
312C LYS* 3.2 7.2 - - + +
314C PHE* 1.3 80.0 - - + +
316C ALA* 1.3 64.6 + - - +
320C GLN 3.4 3.6 + - - -
321C GLY* 2.9 57.9 + - - +
322C ASN 4.0 20.4 - - - +
323C LEU* 4.2 10.3 - - + +
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C LYS* 2.9 17.0 + - + +
313C GLU* 3.8 11.7 - - - +
315C VAL* 1.3 79.5 - - - +
317C LYS* 1.3 64.3 + - + +
320C GLN* 4.7 1.4 + - - -
321C GLY* 4.8 2.0 + - - -
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Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C GLU 3.0 14.8 + - - +
314C PHE 3.4 0.2 - - - -
316C ALA* 1.3 83.2 - - - +
318C GLU* 1.3 88.0 + - + +
319C GLY 2.7 17.2 + - - -
320C GLN* 2.9 14.4 + - - +
360C HIS* 3.8 10.1 - - + -
363C LYS* 4.0 20.4 - - - +
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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