Contacts of the helix formed by residues 358 - 373 (chain B) in PDB entry 4RN1
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 GLU 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B ARG 3.3 10.8 + - - +
357B ASN* 1.3 71.5 - - - +
359B PRO* 1.3 73.9 - - + +
360B HIS* 4.5 3.8 - - + +
361B ARG* 3.1 22.3 + - + +
362B ILE* 3.0 23.3 + - - +
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Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LYS* 5.0 10.3 - - - +
357B ASN 3.7 7.1 - - - +
358B GLU* 1.3 85.5 - - + +
360B HIS* 1.3 57.6 + - - +
362B ILE* 3.5 8.4 + - + +
363B GLN* 3.0 28.6 + - - +
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Residues in contact with HIS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B GLU* 3.2 4.6 + - + -
359B PRO* 1.3 76.7 - - - +
361B ARG* 1.3 57.1 + - + +
363B GLN* 3.2 8.1 + - - +
364B GLN* 2.7 60.4 + - + +
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASP* 4.9 6.7 + - - -
214B VAL* 4.5 15.3 - - - +
230B PRO* 5.7 2.4 - - - +
232B GLN* 6.3 3.1 - - + -
358B GLU* 3.1 26.8 + - + +
360B HIS* 1.3 79.7 - - + +
362B ILE* 1.3 59.5 + - + +
364B GLN* 2.8 41.0 + - - +
365B ILE* 2.9 61.9 + - + +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B VAL* 6.5 0.4 - - + -
230B PRO 5.0 4.9 - - - +
231B ILE* 5.5 0.9 - - + -
239B LYS* 4.7 9.6 - - + -
243B ILE* 3.6 44.4 - - + -
357B ASN* 3.9 32.1 - - + +
358B GLU 3.0 16.8 + - - +
359B PRO* 3.6 10.5 - - + +
361B ARG* 1.3 79.2 - - + +
363B GLN* 1.3 63.4 + - - +
365B ILE* 3.2 17.9 + - + +
366B LEU* 3.0 33.7 + - + +
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Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B PRO 3.0 18.5 + - - +
360B HIS* 3.2 8.9 + - - +
362B ILE* 1.3 76.6 - - - +
364B GLN* 1.3 61.6 + - - +
366B LEU* 3.4 19.4 + - - +
367B ASN* 3.1 59.3 + - - +
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B HIS* 2.7 46.6 + - + +
361B ARG* 2.8 42.3 + - - +
362B ILE 3.2 0.2 - - - -
363B GLN* 1.3 74.7 - - - +
365B ILE* 1.3 60.3 + - - +
367B ASN* 3.5 8.7 + - - +
368B TYR* 3.2 23.1 + - + +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL* 3.8 22.2 - - + -
229B VAL* 4.3 10.8 - - + -
230B PRO* 3.3 43.1 - - + +
361B ARG* 2.9 52.9 + - + +
362B ILE* 3.2 15.2 + - + +
364B GLN* 1.3 75.0 - - - +
366B LEU* 1.3 66.7 + - + +
368B TYR* 3.2 7.5 + - - +
369B ILE* 3.0 34.8 + - + +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLN 5.2 0.7 - - - +
243B ILE* 4.1 24.5 - - + +
246B SER* 4.2 22.2 - - - +
247B VAL* 3.8 28.0 - - + -
362B ILE* 3.0 30.9 + - + +
363B GLN* 3.7 27.1 - - - +
365B ILE* 1.3 79.9 - - + +
367B ASN* 1.3 58.4 + - - +
369B ILE* 3.3 8.6 + - + +
370B LYS* 2.8 30.7 + - + +
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Residues in contact with ASN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B GLN* 3.1 44.6 + - - +
364B GLN* 3.8 7.3 - - - +
365B ILE 3.3 0.2 - - - -
366B LEU* 1.3 74.3 - - - +
368B TYR* 1.3 61.2 + - - +
370B LYS* 3.3 17.3 + - - +
371B GLY* 3.0 24.9 + - - -
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Residues in contact with TYR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL* 3.4 38.8 - - + -
215B SER* 4.0 22.8 + - - -
217B VAL* 5.0 1.0 - - + +
364B GLN* 3.2 14.8 + - + +
365B ILE* 3.5 9.2 - - - +
367B ASN* 1.3 75.6 - - - +
369B ILE* 1.3 60.7 + - - +
371B GLY* 3.4 2.5 + - - -
372B ASN* 3.1 63.3 + - - +
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL* 3.8 13.9 - - + -
227B VAL* 3.8 24.0 - - + -
228B ASN 3.9 9.2 - - - +
229B VAL* 3.7 30.1 - - + -
247B VAL* 4.2 19.5 - - + -
250B GLU* 5.8 1.3 - - + -
365B ILE* 3.0 23.6 + - + +
366B LEU* 3.6 8.3 - - - +
368B TYR* 1.3 74.1 - - - +
370B LYS* 1.3 65.5 + - - +
372B ASN* 3.0 12.1 + - + +
373B LEU* 3.0 40.5 + - + +
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 3.3 46.9 + - + +
366B LEU* 2.8 18.1 + - + +
367B ASN* 3.5 18.4 - - - +
369B ILE* 1.3 77.0 - - - +
371B GLY* 1.3 60.8 + - - +
373B LEU* 3.7 8.3 + - - +
374B LYS* 3.6 17.5 + - - +
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Residues in contact with GLY 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B ASN 3.0 13.2 + - - -
368B TYR* 3.9 4.0 - - - -
370B LYS* 1.3 77.2 - - - +
372B ASN* 1.3 63.7 + - - +
374B LYS* 3.4 13.1 - - - +
375B HIS* 3.3 20.1 + - - -
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Residues in contact with ASN 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL 4.1 3.0 + - - -
217B VAL* 3.5 22.8 - - + +
224B TYR* 3.7 37.4 - - + +
227B VAL* 6.3 1.8 - - + -
368B TYR* 3.1 48.9 + - - +
369B ILE* 3.0 13.9 + - + +
371B GLY* 1.3 78.3 - - - +
373B LEU* 1.3 63.7 + - + +
374B LYS 3.1 0.2 - - - -
375B HIS* 3.2 23.7 + - - +
376B VAL 4.1 0.3 + - - -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B MET* 4.2 14.4 - - + -
224B TYR 4.3 3.8 - - - +
227B VAL* 4.0 21.8 - - + -
247B VAL 4.6 0.7 - - - +
250B GLU* 3.6 31.9 - - + +
251B VAL* 3.7 23.8 - - + +
254B ALA* 3.7 18.4 - - + +
369B ILE* 3.0 32.9 + - + +
370B LYS* 4.2 4.9 - - - +
371B GLY 3.4 0.2 - - - -
372B ASN* 1.3 72.7 - - + +
374B LYS* 1.3 64.2 + - - +
375B HIS 3.1 2.5 - - - -
376B VAL* 3.1 37.7 + - + +
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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