Contacts of the helix formed by residues 280 - 293 (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 THR 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B ASP* 2.3 40.7 + - - +
269B ILE* 3.7 8.2 - - - +
278B ASN 4.9 0.4 - - - +
279B MET* 1.3 79.3 - - - +
281B PRO* 1.3 75.1 - - - +
282B VAL* 3.1 19.7 + - - +
283B GLY 3.2 8.3 + - - -
284B ILE* 3.5 8.5 + - - +
348B ILE* 3.4 26.7 - - + +
350B PRO* 3.8 25.6 - - + -
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 3.8 3.3 - - + -
280B THR* 1.3 88.2 - - - +
282B VAL* 1.3 57.9 + - + +
284B ILE* 3.5 2.8 + - + +
285B GLY 2.9 23.7 + - - -
313B ARG* 4.6 2.7 - - + +
314B CYS* 3.6 47.8 - - + +
317B TYR* 3.3 31.4 - - + -
318B LEU* 3.8 2.4 - - - +
346B LEU 5.4 2.7 - - - +
347B GLU* 6.2 0.2 - - - -
348B ILE* 3.9 33.2 - - + +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 4.4 3.4 - - + +
280B THR* 3.1 14.3 - - - +
281B PRO* 1.3 80.8 - - + +
283B GLY* 1.3 60.6 + - - +
285B GLY* 3.3 1.9 + - - -
286B LYS* 3.2 43.5 + - - +
317B TYR* 3.8 29.6 + - + +
347B GLU* 5.9 7.0 - - + -
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 3.2 35.2 + - - -
240B TYR* 5.2 0.2 - - - -
241B TYR* 4.8 3.3 - - - +
279B MET* 4.1 8.7 - - - -
280B THR 3.2 4.9 + - - -
282B VAL* 1.3 76.3 - - - +
284B ILE* 1.3 64.1 + - - +
286B LYS* 3.3 19.6 + - - +
287B CYS* 3.5 16.1 + - - -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 4.5 12.3 - - + +
240B TYR* 4.2 20.6 - - + +
264B LEU* 3.8 30.7 - - + +
265B GLY 5.8 1.1 - - - +
268B THR* 4.0 15.9 - - - +
269B ILE* 4.2 15.9 - - + -
279B MET* 3.8 18.8 - - + -
280B THR 3.5 12.3 + - - +
281B PRO* 3.5 7.5 + - + +
282B VAL 3.4 0.2 - - - -
283B GLY* 1.3 74.4 - - - +
285B GLY* 1.3 61.7 + - - +
287B CYS* 3.1 7.6 + - - +
288B LEU* 3.0 19.8 + - - +
314B CYS* 5.1 3.6 - - - -
318B LEU* 4.0 17.7 - - + -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO 2.9 18.3 + - - -
282B VAL 3.6 3.6 - - - -
283B GLY 3.2 0.6 - - - -
284B ILE* 1.3 77.1 - - - +
286B LYS* 1.3 55.2 + - - +
288B LEU* 3.2 4.5 + - - +
289B LYS* 2.9 39.0 + - - +
317B TYR* 4.4 7.9 - - - -
318B LEU* 3.6 16.5 - - - +
321B VAL* 4.1 5.5 - - - +
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Residues in contact with LYS 286 (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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237B ASP* 5.9 4.9 - - + +
241B TYR* 3.3 50.1 + - + -
282B VAL* 3.2 32.6 + - + +
283B GLY* 3.6 9.0 - - - +
284B ILE 3.2 0.6 - - - -
285B GLY* 1.3 75.7 - - - +
287B CYS* 1.3 61.6 + - - +
289B LYS* 3.5 17.9 + - + +
290B TYR* 3.2 17.3 + - - +
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Residues in contact with CYS 287 (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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177B LEU* 4.0 13.7 - - + -
240B TYR* 3.9 21.8 - - - -
241B TYR* 4.0 13.9 - - - -
244B CYS* 3.6 41.3 - - - -
248B LEU* 4.7 1.9 - - + +
283B GLY 3.6 14.1 - - - -
284B ILE* 3.1 10.4 + - - +
286B LYS* 1.3 74.9 - - - +
288B LEU* 1.3 64.3 + - - +
290B TYR* 3.3 5.3 + - - +
291B ILE* 3.3 29.3 + - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 5.6 0.4 - - - +
262B LEU* 3.6 32.1 - - + -
264B LEU* 4.7 8.7 - - + +
284B ILE 3.0 11.9 + - - +
285B GLY* 3.4 9.0 - - - +
287B CYS* 1.3 77.6 - - - +
289B LYS* 1.3 56.8 + - - +
291B ILE* 3.2 3.7 + - + +
292B LEU* 2.9 52.9 + - + +
298B THR* 5.8 0.4 - - + -
300B ILE* 4.0 15.5 - - + -
318B LEU* 3.7 42.6 - - + +
321B VAL* 3.8 11.7 - - + -
322B ILE* 3.8 12.6 - - + -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY 2.9 21.9 + - - +
286B LYS* 3.7 17.2 - - + +
288B LEU* 1.3 76.5 - - - +
290B TYR* 1.3 62.5 + - - +
292B LEU* 3.3 9.5 + - + +
293B GLN* 3.0 26.7 + - - +
317B TYR* 5.2 6.3 + - - -
321B VAL* 3.6 34.3 - - + +
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Residues in contact with TYR 290 (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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241B TYR* 4.1 12.1 - - + +
245B GLU* 3.7 39.3 - - + +
248B LEU* 4.0 24.2 - - + -
249B LYS* 3.4 27.4 - - - +
286B LYS 3.2 11.9 + - - +
287B CYS* 3.6 9.9 - - - +
288B LEU 3.3 0.4 - - - -
289B LYS* 1.3 78.9 - - - +
291B ILE* 1.3 59.2 + - - +
293B GLN* 2.9 45.7 + - + +
294B TRP* 3.7 32.5 + + - -
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Residues in contact with ILE 291 (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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175B VAL* 4.3 14.6 - - + -
177B LEU* 5.6 2.2 - - + -
248B LEU* 3.8 25.8 - - + -
260B VAL* 3.8 27.9 - - + +
262B LEU* 3.8 37.7 - - + -
287B CYS* 3.4 15.0 - - + +
288B LEU* 3.2 7.9 + - + +
289B LYS 3.2 0.2 - - - -
290B TYR* 1.3 77.2 - - - +
292B LEU* 1.3 65.3 + - + +
294B TRP* 3.2 39.5 + - + +
295B GLN 4.1 1.0 + - - -
296B LEU 5.1 0.9 + - - -
298B THR* 4.7 14.2 + - + +
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Residues in contact with LEU 292 (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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133B VAL* 3.9 29.6 - - + -
288B LEU* 2.9 45.8 + - + +
289B LYS* 3.3 9.4 + - + +
291B ILE* 1.3 79.6 - - + +
293B GLN* 1.3 56.2 + - - +
295B GLN* 2.8 26.0 + - - +
296B LEU 6.1 0.2 - - - +
298B THR* 4.7 17.0 - - + +
300B ILE* 5.3 0.4 - - + -
321B VAL* 4.5 6.5 - - + +
322B ILE* 4.0 28.3 - - + +
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Residues in contact with GLN 293 (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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289B LYS 3.0 13.7 + - - +
290B TYR* 2.9 46.9 + - + +
292B LEU* 1.3 72.2 - - - +
294B TRP* 1.3 84.1 + - - +
295B GLN* 3.1 18.1 + - - +
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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