Contacts of the helix formed by residues 317 - 334 (chain B) in PDB entry 4ROE
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 VAL 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B GLU* 5.5 0.7 - - - -
258B MET* 3.5 7.4 - - - -
315B ALA* 3.5 5.7 - - - +
316B LYS* 1.4 83.8 - - + +
318B ARG* 1.3 65.3 + - - +
319B ALA* 4.4 10.3 - - + +
320B GLU* 3.0 48.4 + - + +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.7 25.6 - - + +
225B LYS 5.1 0.4 + - - -
226B SER* 4.0 13.7 - - - -
227B GLU* 3.0 40.9 + - - +
228B GLU* 4.2 5.1 + - - -
258B MET* 3.4 14.1 - - + +
317B VAL* 1.3 70.2 - - - +
319B ALA* 1.3 60.9 + - - +
321B ILE* 3.1 20.0 + - - +
322B TYR* 3.2 52.5 + - + +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 3.1 12.0 + - + +
318B ARG* 1.3 77.7 - - - +
320B GLU* 1.4 56.2 + - + +
322B TYR* 3.4 12.4 + - - +
323B GLU* 2.9 33.6 + - - +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PRO* 3.4 26.0 - - + +
299B ARG 5.3 2.1 - - - +
300B ILE* 3.6 18.2 - - + +
314B GLY 4.5 1.0 - - - +
315B ALA* 3.3 6.2 - - + -
316B LYS* 2.9 31.8 + - - +
317B VAL* 3.0 29.5 + - + +
319B ALA* 1.4 74.5 - - + +
321B ILE* 1.3 59.6 + - - +
323B GLU* 4.2 4.7 - - - +
324B ALA* 3.1 30.0 + - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PRO* 3.8 26.2 - - + +
165B LEU* 4.4 20.9 - - + -
258B MET* 3.5 19.7 - - + +
260B GLY* 4.0 15.9 - - - +
300B ILE* 4.6 4.5 - - + -
312B LEU* 3.4 47.1 - - + +
313B THR* 4.2 2.2 - - - +
315B ALA* 3.6 20.9 - - + +
317B VAL 4.8 0.9 - - - +
318B ARG 3.1 12.5 + - - +
320B GLU* 1.3 75.7 - - - +
322B TYR* 1.3 61.5 + - + +
324B ALA* 4.7 0.4 - - - -
325B PHE* 3.1 25.3 + - - +
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Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 3.9 20.8 - - + +
163B PRO* 3.6 44.0 + - + -
165B LEU* 5.3 3.1 - - + +
318B ARG* 3.2 60.4 + - + +
319B ALA* 3.7 12.3 - - - +
321B ILE* 1.3 80.9 - - + +
323B GLU* 1.4 54.8 + - - +
325B PHE* 3.4 2.1 + - - +
326B GLU* 3.0 37.6 + - + +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LYS* 4.5 12.8 - - - +
298B PRO* 3.9 34.1 - - + +
319B ALA* 2.9 20.2 + - - +
320B GLU* 4.9 3.8 - - - +
322B TYR* 1.4 74.9 - - - +
324B ALA* 1.4 55.8 + - - +
326B GLU* 3.4 6.6 + - - +
327B ASN* 3.1 42.2 + - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 3.4 31.7 - - + +
298B PRO* 3.8 2.6 - - + +
300B ILE* 3.7 29.6 - - + -
302B LEU* 4.2 2.0 - - + +
312B LEU* 3.8 10.1 - - + -
320B GLU 3.1 20.0 + - - +
323B GLU* 1.4 73.4 - - - +
325B PHE* 1.4 59.7 + - - +
327B ASN 3.4 0.7 + - - -
328B ILE* 3.0 26.0 + - - +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B SER* 3.3 23.8 - - - -
161B ILE* 3.5 34.5 - - + -
163B PRO* 3.6 22.0 - - + -
262B CYS* 3.4 22.2 - - - -
264B VAL* 3.8 21.5 - - + -
310B VAL* 4.8 4.7 - - + -
312B LEU* 3.6 10.3 - - + +
321B ILE 3.1 17.8 + - - +
322B TYR 3.4 2.0 + - - +
324B ALA* 1.4 72.6 - - - +
326B GLU* 1.3 73.2 + - - +
328B ILE* 3.4 17.6 - - + +
329B TYR* 3.0 46.5 + + - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO* 3.6 15.8 - - - +
159B SER* 3.0 42.9 + - - -
160B GLY 5.0 0.3 + - - -
161B ILE 3.8 5.7 - - - +
163B PRO* 5.6 0.7 - - - +
322B TYR* 3.0 22.9 + - + +
323B GLU* 3.9 6.5 - - - +
325B PHE* 1.3 89.2 - - - +
327B ASN* 1.3 59.0 + - - +
329B TYR* 4.1 2.6 - - - +
330B PRO* 3.1 25.1 - - - +
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Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 3.8 15.5 - - + +
297B LYS 2.9 27.9 + - - -
298B PRO* 3.9 3.4 - - - +
323B GLU* 3.1 29.0 + - - +
324B ALA 3.6 4.7 - - - +
325B PHE 3.3 0.2 - - - -
326B GLU* 1.3 78.1 - - - +
328B ILE* 1.4 60.1 + - - +
330B PRO* 3.4 15.0 - - - +
331B ILE* 3.5 18.0 - - + +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 6.0 0.2 - - + -
293B TYR* 3.7 50.7 - - + +
295B MET* 3.8 7.4 - - + +
302B LEU* 3.7 21.1 - - + -
304B ILE* 4.2 10.8 - - + -
310B VAL* 4.9 2.2 - - + -
324B ALA 3.0 15.7 + - - +
325B PHE* 3.4 25.8 - - + +
327B ASN* 1.4 77.0 - - - +
329B TYR* 1.3 68.1 + - - +
330B PRO 3.5 0.2 - - - -
331B ILE* 3.0 16.8 + - + +
332B LEU* 3.0 43.3 + - + +
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO 5.5 0.4 - - - -
159B SER* 3.5 34.8 + - - -
161B ILE* 3.6 24.2 - - + +
264B VAL* 3.7 32.7 + - + -
266B PHE* 3.9 12.5 - + - -
325B PHE* 3.0 28.8 + + + +
326B GLU* 4.1 4.3 - - - +
328B ILE* 1.3 77.2 - - - +
330B PRO* 1.4 65.0 - - + +
332B LEU* 3.2 6.0 + - - +
333B LYS* 2.8 74.8 + - + +
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Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLU 3.1 26.9 - - - +
327B ASN* 3.4 15.7 - - - +
329B TYR* 1.4 86.0 - - + +
331B ILE* 1.3 54.3 + - + +
333B LYS* 4.2 7.0 - - + -
334B GLY* 2.8 30.3 + - - -
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 3.7 22.8 - - + +
277B HIS* 3.5 40.1 - - + +
293B TYR* 3.8 20.4 - - + +
295B MET* 5.5 2.5 - - + -
327B ASN* 3.5 21.3 - - + +
328B ILE* 3.0 23.4 + - + +
330B PRO* 1.3 78.3 - - + +
332B LEU* 1.3 59.2 + - + +
334B GLY 3.2 19.7 - - - +
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Residues in contact with LEU 332 (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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264B VAL* 4.1 14.6 - - + -
266B PHE* 3.3 19.7 - - + -
268B ILE* 4.0 27.8 - - + +
273B LEU* 3.9 29.2 - - + -
304B ILE* 3.9 20.4 - - + -
310B VAL* 4.1 26.5 - - + -
328B ILE* 3.0 34.9 + - + +
329B TYR* 3.7 6.7 - - - +
331B ILE* 1.3 77.9 - - + +
333B LYS* 1.3 63.1 + - - +
334B GLY 4.5 1.9 - - - -
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.6 22.9 - - + -
329B TYR* 2.8 57.6 + - + +
330B PRO* 4.1 6.3 - - + +
332B LEU* 1.3 74.9 - - - +
334B GLY* 1.3 60.5 + - - +
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Residues in contact with GLY 334 (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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330B PRO 2.8 20.3 + - - +
331B ILE* 3.2 17.3 - - - +
332B LEU 4.5 1.8 - - - -
333B LYS* 1.3 77.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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