Contacts of the helix formed by residues 289 - 306 (chain B) in PDB entry 4IYM
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 GLY 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B PRO* 5.5 1.3 - - - -
287B PRO 4.5 1.2 - - - +
288B VAL* 1.3 78.0 + - - +
290B GLU* 1.3 66.5 + - - -
291B GLU 3.4 2.2 - - - -
292B THR* 3.6 1.5 + - - -
293B ALA* 3.1 23.0 + - - +
391B ARG* 6.0 1.2 - - - +
392B ALA 3.0 16.1 + - - -
393B ARG* 4.4 9.6 + - - -
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY* 1.3 69.9 - - - -
291B GLU* 1.3 60.4 + - - +
293B ALA* 3.2 2.4 + - - +
294B ASN* 2.8 48.7 + - - +
391B ARG* 3.0 42.7 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY* 3.4 0.6 - - - -
290B GLU* 1.3 77.7 - - - +
292B THR* 1.3 58.0 + - - +
294B ASN* 4.0 5.7 - - - +
295B ARG* 3.0 60.2 + - + +
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Residues in contact with THR 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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254B ILE* 3.8 26.5 - - + +
255B MSE 4.2 2.9 - - - +
256B PRO* 3.3 21.0 + - - +
260B LEU* 3.8 32.6 - - + +
287B PRO* 4.0 9.2 - - + -
288B VAL 3.0 23.9 + - - -
289B GLY* 3.6 1.3 + - - -
291B GLU* 1.3 78.2 + - - +
293B ALA* 1.3 57.4 + - - +
295B ARG* 4.2 0.3 - - - +
296B LEU* 3.0 32.2 + - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO* 3.6 29.4 - - + +
289B GLY 3.1 17.8 + - - +
290B GLU* 3.2 2.2 + - - +
292B THR* 1.3 77.3 - - - +
294B ASN* 1.3 57.8 + - - +
296B LEU* 3.6 2.4 - - - +
297B ILE* 2.9 35.1 + - - +
389B VAL* 5.4 1.3 - - + -
391B ARG* 3.4 36.6 - - + +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 2.8 37.5 + - - +
291B GLU* 4.1 5.4 - - - +
293B ALA* 1.3 71.9 - - - +
295B ARG* 1.3 58.9 + - + +
297B ILE* 3.3 5.5 + - - +
298B ASP* 2.9 27.4 + - - +
391B ARG* 2.8 32.5 + - - +
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 3.5 34.8 - - + +
291B GLU* 3.0 47.5 + - + +
292B THR 4.2 2.0 - - - +
294B ASN* 1.3 76.2 - - + +
296B LEU* 1.3 63.1 + - - +
298B ASP* 3.1 9.7 + - + +
299B LYS* 3.0 48.1 + - + +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.6 31.4 - - + -
260B LEU* 4.2 22.2 - - + +
263B ALA* 4.5 7.6 - - + -
264B ALA* 4.1 28.5 - - + +
267B LEU* 3.8 13.0 - - + -
285B ALA* 4.7 4.0 - - + -
287B PRO* 4.2 16.4 - - + -
292B THR 3.0 18.6 + - - +
293B ALA* 3.6 4.9 - - - +
295B ARG* 1.3 76.1 - - - +
297B ILE* 1.3 57.5 + - + +
299B LYS* 3.2 7.7 + - + +
300B LEU* 2.9 45.2 + - + +
389B VAL* 5.6 2.5 - - + -
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 2.9 21.7 + - - +
294B ASN* 3.7 6.3 - - - +
296B LEU* 1.3 75.6 - - + +
298B ASP* 1.3 62.6 + - - +
300B LEU* 4.5 4.9 - - + +
301B VAL* 3.1 40.8 + - + +
346B VAL* 4.8 10.8 - - + -
367B LEU* 4.7 12.1 - - + -
369B ASP* 3.7 37.2 - - + +
389B VAL* 4.0 27.1 - - + -
391B ARG* 4.1 6.7 - - - +
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASN 2.9 14.4 + - - +
295B ARG* 3.1 15.7 + - + +
297B ILE* 1.3 76.1 - - - +
299B LYS* 1.3 58.3 + - + +
301B VAL* 4.9 0.8 - - - +
302B PRO* 3.3 23.6 - - - +
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 3.7 20.2 - - + +
261B ASP* 2.9 47.8 + - - +
264B ALA* 3.9 13.0 - - + -
295B ARG* 3.0 39.9 + - + +
296B LEU* 3.8 8.1 - - - +
297B ILE 3.2 0.2 - - - -
298B ASP* 1.3 78.6 - - + +
300B LEU* 1.3 64.6 + - - +
302B PRO* 3.5 14.5 - - - +
303B MSE 3.4 21.1 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 3.7 30.7 - - + +
267B LEU* 3.8 25.6 - - + -
268B ILE* 4.0 14.6 - - + -
296B LEU* 2.9 41.5 + - + +
297B ILE* 4.2 4.3 - - + +
299B LYS* 1.3 76.3 - - - +
301B VAL* 1.3 65.9 + - - +
303B MSE 3.1 5.9 + - - +
304B VAL* 2.9 28.5 + - + +
367B LEU* 3.8 29.2 - - + -
387B LEU* 4.7 6.7 - - + -
389B VAL* 4.9 9.2 - - + -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.1 34.0 + - + +
298B ASP* 4.9 0.9 - - - +
300B LEU* 1.3 74.8 - - - +
302B PRO* 1.4 71.3 - - + +
304B VAL 3.4 0.2 + - - -
305B GLU* 3.1 50.5 + - - +
346B VAL* 4.1 26.0 - - + +
347B VAL* 4.0 14.8 - - + +
367B LEU* 4.3 2.9 - - + -
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Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASP 3.3 21.5 - - - +
299B LYS* 3.5 11.9 - - - +
301B VAL* 1.4 93.9 - - + +
303B MSE 1.3 60.5 + - + +
305B GLU* 3.5 13.4 + - - +
306B SER* 3.1 30.4 + - - -
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Residues in contact with MSE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASP 5.6 0.2 - - - +
264B ALA* 3.9 24.5 - - + -
265B ASN* 3.5 24.9 - - - +
268B ILE* 3.8 35.4 - - + +
299B LYS* 3.4 25.1 - - + +
300B LEU* 3.1 4.8 + - - +
302B PRO* 1.3 79.1 - - + +
304B VAL* 1.3 63.9 + - - +
306B SER* 3.5 9.1 + - - +
307B LEU* 3.4 24.4 + - - +
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Residues in contact with VAL 304 (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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268B ILE* 3.6 9.4 - - + -
272B TYR* 3.5 47.8 - - + +
300B LEU* 2.9 23.5 + - + +
301B VAL 4.0 2.7 - - - +
303B MSE 1.3 72.6 - - - +
305B GLU* 1.3 64.9 + - - +
306B SER 3.4 0.3 + - - -
307B LEU* 3.5 22.9 + - + +
347B VAL* 3.6 27.4 - - + +
365B GLY* 4.0 19.0 + - - +
366B CYS 4.6 0.4 - - - -
367B LEU* 4.3 10.5 - - + -
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 3.1 37.5 + - - +
302B PRO* 3.6 12.1 - - - +
304B VAL* 1.3 79.1 - - - +
306B SER* 1.3 57.0 + - - +
307B LEU 3.8 3.8 + - - +
346B VAL 4.8 3.5 - - - +
347B VAL* 3.9 23.6 - - + +
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Residues in contact with SER 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO 3.1 18.1 + - - -
303B MSE 3.5 11.3 + - - +
304B VAL 3.2 0.6 - - - -
305B GLU* 1.3 76.9 - - - +
307B LEU* 1.3 66.1 + - - +
308B ARG* 3.2 5.7 + - - +
318B ASP* 4.2 2.1 - - - +
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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
------------------------------------------------------------
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