Contacts of the helix formed by residues 286 - 298 (chain B) in PDB entry 4FG8
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 ILE 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 2.7 28.9 + - + +
114B THR 4.2 1.8 - - - -
115B GLU* 4.1 15.5 - - + +
212B LEU* 4.0 28.0 - - + +
244B ASP* 5.0 15.0 - - + +
245B ILE* 4.0 30.5 - - + -
284B LYS* 3.1 18.3 + - + +
285B ASN* 1.3 75.1 - - - +
287B HIS* 1.3 67.4 + - - +
288B GLN* 3.2 3.2 + - - -
289B SER* 3.7 7.4 + - - -
290B VAL* 3.3 24.3 + - + +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 3.0 26.2 + - + -
108B VAL 3.1 16.3 + - - -
109B GLU 5.0 0.2 - - - -
110B LYS 2.9 27.7 + - - -
111B GLY* 4.0 10.4 + - - +
113B TYR* 3.4 31.3 + + + +
285B ASN* 3.0 20.9 + - - +
286B ILE* 1.3 77.4 - - - +
288B GLN* 1.3 62.1 + - - +
290B VAL* 3.2 1.4 + - - -
291B SER* 2.8 52.3 + - - -
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 4.8 1.2 + - - -
286B ILE 3.2 1.6 + - - -
287B HIS* 1.3 82.0 + - - +
289B SER* 1.3 70.5 + - - +
291B SER* 3.9 3.1 - - - -
292B GLU* 3.1 51.1 + - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B CYS 4.5 1.8 + - - -
241B TYR* 3.9 29.7 - - - +
286B ILE* 3.7 7.6 + - - -
287B HIS 3.5 0.2 - - - -
288B GLN* 1.3 88.0 - - - +
290B VAL* 1.3 64.4 + - - +
292B GLU* 3.4 11.0 + - - +
293B GLN* 3.0 29.3 + - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.3 5.6 - - + -
113B TYR* 4.2 20.6 - - + -
210B ILE 4.5 0.9 - - - +
211B LEU* 4.3 5.6 - - - +
212B LEU 3.5 31.6 - - - +
213B CYS* 3.8 9.9 - - - +
214B GLY* 3.6 11.3 - - - +
286B ILE* 3.3 29.5 + - + +
287B HIS* 3.2 4.7 + - + +
289B SER* 1.3 79.5 - - - +
291B SER* 1.3 59.0 + - - +
293B GLN 3.2 1.2 + - - -
294B ILE* 2.8 49.6 + - + +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 5.6 0.7 - - - -
108B VAL* 4.1 22.5 + - - +
287B HIS* 2.8 47.5 + - - -
288B GLN* 3.9 3.6 - - - -
290B VAL* 1.3 73.6 - - - +
292B GLU* 1.3 63.8 + - - +
294B ILE* 3.3 4.0 + - - +
295B LYS* 3.1 45.3 + - - +
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Residues in contact with GLU 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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241B TYR* 5.9 1.4 - - - -
288B GLN* 3.1 38.3 + - - +
289B SER* 3.5 11.5 + - - +
290B VAL 3.2 0.2 - - - -
291B SER* 1.3 82.0 + - - +
293B GLN* 1.3 68.2 + - - +
295B LYS* 3.6 10.2 + - - +
296B LYS* 3.3 43.1 + - + +
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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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213B CYS 3.3 24.2 - - - +
214B GLY 3.2 10.7 - - - +
215B TYR* 3.7 16.5 - - + +
241B TYR* 3.5 32.1 + - + -
289B SER* 3.0 17.2 + - - +
290B VAL 3.7 0.4 - - - +
292B GLU* 1.3 80.4 - - + +
294B ILE* 1.3 60.8 + - - +
296B LYS* 3.1 32.4 + - - +
297B ASN* 2.8 50.6 + - - +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.7 47.8 - - + +
107B ILE* 3.9 21.3 - - + -
108B VAL* 3.7 20.4 - - + -
210B ILE 5.3 1.6 - - - +
211B LEU* 6.2 1.3 - - + -
214B GLY* 3.4 20.4 - - - +
290B VAL* 2.8 36.4 + - + +
291B SER* 3.3 4.7 + - - +
293B GLN* 1.3 75.3 - - - +
295B LYS* 1.3 64.8 + - - +
298B PHE* 3.0 36.0 + - + +
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Residues in contact with LYS 295 (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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108B VAL* 3.8 31.0 - - + +
291B SER* 3.1 24.4 + - - +
292B GLU* 3.7 11.0 - - - +
294B ILE* 1.3 77.0 - - - +
296B LYS* 1.3 60.5 + - + +
298B PHE 4.3 3.0 + - - -
299B ALA* 4.3 15.1 + - - +
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 4.8 5.9 + - - -
292B GLU* 3.3 29.1 + - + +
293B GLN* 3.1 40.9 + - - +
295B LYS* 1.3 78.1 - - + +
297B ASN* 1.3 67.1 + - - +
299B ALA* 5.2 2.9 + - - +
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Residues in contact with ASN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLY 3.9 3.1 - - - +
215B TYR* 3.5 18.1 - - - +
216B PRO* 3.9 17.8 - - + +
219B TYR* 5.8 3.8 - - - +
293B GLN* 2.8 45.5 + - - +
296B LYS* 1.3 84.9 + - - +
298B PHE* 1.3 79.3 + - + +
299B ALA 3.8 1.8 - - - -
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Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.5 33.1 - + + +
145B GLU* 5.0 5.4 - - - +
184B TYR* 3.6 20.4 - - - -
210B ILE* 3.6 34.1 - - + -
214B GLY 3.5 21.8 - - - -
216B PRO* 3.5 30.3 - - + -
294B ILE* 3.0 26.1 + - + +
295B LYS* 4.9 0.4 - - - -
297B ASN* 1.3 87.9 - - + +
299B ALA* 1.3 65.3 + - - +
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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
------------------------------------------------------------
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