Contacts of the helix formed by residues 303 - 316 (chain A) in PDB entry 1R4L
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 ASP 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ALA 4.6 4.9 - - - +
302A TRP* 1.3 75.3 - - - +
304A ALA* 1.3 71.9 + - + +
305A GLN* 4.4 9.1 - - - +
306A ARG* 2.9 30.1 + - - +
307A ILE* 3.1 25.8 + - - +
364A VAL* 4.4 6.3 - - - -
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Residues in contact with ALA 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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303A ASP* 1.3 74.6 - - - +
305A GLN* 1.3 68.7 + - - +
307A ILE* 2.7 21.8 + - - +
308A PHE* 3.1 8.6 + - - -
333A LEU* 3.4 35.4 - - + +
334A THR* 3.7 16.3 - - + +
362A THR* 4.2 16.6 - - - -
364A VAL* 5.2 1.2 - - - +
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Residues in contact with GLN 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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303A ASP* 3.5 10.4 - - - +
304A ALA* 1.3 77.8 - - - +
306A ARG* 1.3 69.2 + - - +
307A ILE 2.6 2.4 + - - -
308A PHE* 2.9 3.9 + - - +
309A LYS* 2.7 37.2 + - + +
328A TRP* 3.8 36.1 - - + -
333A LEU* 5.0 3.7 - - + +
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Residues in contact with ARG 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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300A GLN* 3.8 17.2 + - - +
301A ALA 5.5 0.2 + - - -
302A TRP* 2.8 70.3 - - + +
303A ASP* 2.9 27.0 + - - +
305A GLN* 1.3 78.7 - - - +
307A ILE* 1.3 57.3 + - - +
309A LYS* 3.5 7.6 - - - +
310A GLU* 2.8 48.1 + - - +
421A ILE 5.2 4.8 + - - -
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Residues in contact with ILE 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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297A MET* 3.5 24.2 - - + -
302A TRP* 3.8 24.0 - - + -
303A ASP 3.1 17.2 + - - +
304A ALA* 2.7 11.1 + - - +
305A GLN 2.6 4.0 + - - -
306A ARG* 1.3 66.4 - - - +
308A PHE* 1.3 59.9 + - + +
309A LYS 2.7 14.0 + - - -
310A GLU* 2.8 14.4 + - - +
311A ALA* 2.8 13.6 + - + +
362A THR* 4.2 9.2 - - + -
363A LYS 3.9 20.0 - - - +
364A VAL* 4.5 4.5 - - + -
368A ASP 3.9 11.0 - - - +
369A PHE* 4.2 15.2 - - + +
372A ALA* 3.9 24.2 - - + -
373A HIS* 5.5 0.3 - - - -
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Residues in contact with PHE 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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304A ALA 3.1 9.7 + - - +
305A GLN 2.9 8.0 + - - +
307A ILE* 1.3 79.3 - - + +
309A LYS* 1.3 56.2 + - - +
311A ALA* 3.9 7.6 - - - -
312A GLU* 3.3 23.1 + - - +
327A PHE* 4.5 4.0 - + + -
328A TRP* 3.7 17.1 - - + -
333A LEU* 3.8 33.4 - - + -
358A ILE* 4.1 26.7 - - + -
360A MET* 3.5 25.4 - - - -
362A THR* 3.2 31.9 - - + -
372A ALA* 3.9 24.7 - - + -
375A GLU* 4.9 0.9 - - + -
376A MET* 3.6 26.3 - - + +
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Residues in contact with LYS 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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305A GLN* 2.7 28.1 + - + +
306A ARG* 3.5 10.1 - - - +
308A PHE* 1.3 77.3 - - - +
310A GLU* 1.3 62.5 - - - +
311A ALA 3.1 1.6 - - - -
312A GLU* 3.6 15.1 + - - +
313A LYS* 3.1 27.0 + - - +
328A TRP* 3.2 49.1 - - + +
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Residues in contact with GLU 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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302A TRP* 3.5 24.6 - - + -
306A ARG* 2.8 43.3 + - - +
307A ILE 2.8 4.6 + - - +
309A LYS* 1.3 77.2 - - - +
311A ALA* 1.3 60.4 + - - +
313A LYS* 3.5 22.0 - - - +
314A PHE* 3.8 5.5 + - - +
369A PHE* 4.9 9.0 - - + -
373A HIS* 4.5 5.6 + - - -
417A HIS* 5.7 2.1 + - - -
421A ILE* 2.7 42.9 - - + +
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Residues in contact with ALA 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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307A ILE* 2.8 14.1 + - + +
308A PHE* 4.1 7.2 - - - -
310A GLU* 1.3 74.7 - - - +
312A GLU* 1.3 55.5 + - - +
313A LYS 2.9 4.7 - - - -
314A PHE* 2.6 32.6 + - - +
315A PHE* 3.6 7.0 + - + -
372A ALA* 4.4 11.2 - - + -
373A HIS* 3.4 37.6 + - + +
376A MET* 3.9 13.7 - - - -
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Residues in contact with GLU 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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308A PHE 3.3 15.7 + - - +
309A LYS* 4.0 26.1 - - - +
311A ALA* 1.3 78.9 - - - +
313A LYS* 1.3 61.0 + - - +
314A PHE 3.3 0.7 + - - -
315A PHE* 3.7 6.8 + - - +
316A VAL* 3.3 20.8 + - - +
321A PRO 4.9 0.7 - - - +
322A ASN* 3.8 16.3 - - + +
323A MET* 2.8 43.0 + - + +
328A TRP* 3.1 24.5 + - - -
376A MET* 3.3 18.6 - - - -
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Residues in contact with LYS 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 LYS 3.1 18.8 + - - +
310A GLU* 3.5 23.8 - - - +
312A GLU* 1.3 81.3 - - - +
314A PHE* 1.3 60.0 + - - +
316A VAL* 2.8 30.9 - - + +
317A SER* 3.4 19.6 + - - +
421A ILE* 5.6 3.6 - - + -
546A ASN* 4.7 6.7 - - - +
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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 GLU 3.8 3.9 + - - +
311A ALA 2.6 22.0 + - - +
313A LYS* 1.3 72.1 - - - +
315A PHE* 1.3 61.7 + + + +
317A SER* 2.6 31.5 + - - -
318A VAL* 3.4 6.9 + - + +
373A HIS* 4.2 13.0 - + + +
408A MET* 3.3 54.7 - - + -
411A SER* 3.3 27.8 - - - -
412A ALA* 4.1 15.3 - - + -
417A HIS* 4.0 20.4 - + - -
544A ILE* 3.7 12.1 - - + -
545A SER* 3.2 31.2 - - - -
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Residues in contact with PHE 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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311A ALA 3.6 11.9 + - - -
312A GLU* 3.7 5.1 + - - +
314A PHE* 1.3 77.7 - - + +
316A VAL* 1.3 61.5 + - - +
318A VAL* 3.0 28.7 + - + +
320A LEU* 3.2 18.5 + - + +
321A PRO 4.5 0.2 - - - +
373A HIS* 3.7 11.0 - + + -
376A MET* 3.4 39.3 - - + -
377A GLY* 3.5 31.0 - - - -
380A GLN* 2.8 38.4 - - + +
404A VAL* 5.6 3.8 - - + -
408A MET* 3.3 41.1 - - + -
554A LEU* 6.3 3.1 - - + -
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Residues in contact with VAL 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 GLU* 3.3 10.1 + - + +
313A LYS* 2.8 48.7 - - + +
315A PHE* 1.3 79.2 - - - +
317A SER* 1.3 60.5 + - - +
318A VAL 3.2 0.6 + - - -
319A GLY 3.8 9.5 + - - +
320A LEU 3.1 14.7 + - - +
321A PRO* 4.3 2.7 + - + +
322A ASN* 2.9 30.3 - - - +
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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