Contacts of the helix formed by residues 286 - 298 (chain A) in PDB entry 4FG9
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 2.8 27.2 + - + +
114A THR* 4.1 5.6 - - - -
115A GLU* 4.1 17.5 - - + +
212A LEU* 4.0 19.7 - - + +
244A ASP* 4.2 24.2 - - + +
245A ILE* 3.7 29.4 - - + -
284A LYS* 2.9 25.1 + - + +
285A ASN* 1.3 72.9 - - - +
287A HIS* 1.3 62.1 + - - +
288A GLN 3.8 0.9 - - - -
289A SER* 4.2 5.4 + - - -
290A VAL* 3.2 30.0 + - + +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 2.9 23.5 + - + -
108A VAL 3.8 7.2 + - - -
110A LYS 2.6 30.8 + - - -
111A GLY* 3.5 17.9 + - - +
113A TYR* 3.6 30.6 + - + +
285A ASN* 3.2 18.2 + - - +
286A ILE* 1.3 75.6 - - - +
288A GLN* 1.3 63.4 + - - +
289A SER 3.1 0.9 + - - -
290A VAL* 3.1 1.7 + - - +
291A SER* 2.8 58.6 + - - -
305A GLN* 5.0 4.3 - - - -
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 4.8 1.0 + - - -
286A ILE 3.8 0.2 - - - -
287A HIS* 1.3 85.8 + - - +
289A SER* 1.3 57.2 + - - +
291A SER* 3.8 3.0 - - - -
292A GLU* 3.0 41.8 + - + +
225B LYS* 4.0 21.2 - - - +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A CYS 4.7 2.3 + - - -
241A TYR* 3.9 28.4 + - - +
286A ILE* 4.2 7.3 + - - -
287A HIS 3.2 0.8 - - - -
288A GLN* 1.3 76.3 - - - +
290A VAL* 1.3 67.8 + - - +
292A GLU* 3.4 6.2 + - - +
293A GLN* 3.0 28.0 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.7 3.6 - - + -
113A TYR* 4.3 13.0 - - + -
210A ILE 4.2 6.1 - - - +
211A LEU* 4.2 10.3 - - - +
212A LEU* 3.4 28.3 - - - +
213A CYS* 3.5 11.2 - - - +
214A GLY* 3.6 12.4 - - - +
286A ILE* 3.2 30.7 + - + +
287A HIS* 3.1 2.7 + - + +
289A SER* 1.3 77.4 - - - +
291A SER* 1.3 57.5 + - - +
293A GLN 3.4 0.7 + - - -
294A ILE* 3.0 46.6 + - + +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.8 1.1 - - - -
108A VAL* 3.5 28.1 + - - +
287A HIS* 2.8 42.8 + - - -
288A GLN* 3.8 3.8 - - - -
290A VAL* 1.3 73.2 - - - +
292A GLU* 1.3 56.7 + - - +
294A ILE* 3.3 5.0 + - - +
295A LYS* 3.0 31.3 + - - +
305A GLN* 3.5 21.7 + - - -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLN* 3.0 32.6 + - + +
289A SER* 3.9 5.3 - - - +
291A SER* 1.3 76.7 - - - +
293A GLN* 1.3 61.1 + - + +
295A LYS* 3.3 25.3 + - - +
296A LYS* 3.0 33.1 + - - +
222B ASN* 5.1 4.0 + - - +
225B LYS* 3.1 40.0 + - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A CYS 3.4 24.2 - - - +
214A GLY* 3.3 11.2 - - - -
215A TYR* 3.4 21.1 - - + +
241A TYR* 3.6 34.0 + - + -
289A SER* 3.0 21.0 + - - +
292A GLU* 1.3 77.9 - - - +
294A ILE* 1.3 58.0 + - - +
296A LYS* 3.3 29.5 + - - +
297A ASN* 2.6 46.5 + - - +
220B ASP* 5.1 1.8 + - - -
225B LYS* 6.2 0.8 - - - +
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.9 32.5 - - + -
107A ILE* 4.2 17.3 - - + -
108A VAL* 3.7 14.6 - - + -
210A ILE* 4.8 2.9 - - + +
211A LEU* 6.1 0.9 - - + -
214A GLY* 3.4 19.5 - - - +
290A VAL* 3.0 39.3 + - + +
291A SER 3.3 4.2 + - - +
293A GLN* 1.3 73.0 - - - +
295A LYS* 1.3 58.3 + - - +
298A PHE* 2.8 50.5 + - + +
301A SER* 3.4 22.0 - - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.0 12.3 - - + -
291A SER* 3.0 21.0 + - - +
292A GLU* 3.3 27.1 + - - +
294A ILE* 1.3 75.6 - - - +
296A LYS* 1.3 60.2 + - - +
298A PHE 3.4 11.9 - - - +
299A ALA* 5.1 1.0 - - - -
301A SER* 4.2 1.8 - - - -
302A LYS* 3.8 61.4 + - + +
305A GLN* 2.8 45.5 + - + +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 5.4 0.8 + - - -
292A GLU* 3.0 20.4 + - - +
293A GLN* 3.5 35.2 - - - +
295A LYS* 1.3 78.9 - - - +
297A ASN* 1.3 67.3 + - - +
298A PHE 3.5 1.4 + - - -
302A LYS* 5.9 0.4 - - - -
219B TYR* 5.2 10.8 + - + +
220B ASP* 3.5 28.2 + - - +
221B GLU* 3.8 26.4 - - + +
225B LYS* 5.7 0.8 - - - +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.2 29.0 - - - +
216A PRO* 4.1 17.5 - - + +
293A GLN* 2.6 40.7 + - - +
296A LYS* 1.3 84.9 - - - +
298A PHE* 1.3 79.4 + - + +
299A ALA 4.3 0.2 - - - -
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.9 24.9 - + + -
184A TYR* 3.9 18.8 - - - -
210A ILE* 3.9 17.5 - - + -
214A GLY 3.6 20.6 - - - -
216A PRO* 4.1 17.3 - - + -
294A ILE* 2.8 33.4 + - + +
295A LYS 3.4 15.3 - - - +
296A LYS 3.5 1.5 - - - -
297A ASN* 1.3 89.0 - - + +
299A ALA* 1.3 65.8 + - - +
300A LYS* 3.4 4.0 - - + +
301A SER* 3.4 22.7 + - - +
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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