Contacts of the helix formed by residues 280 - 285 (chain B) in PDB entry 4FGU
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TYR* 5.7 0.2 - - + -
246B LEU* 3.3 41.7 - - + +
249B GLU* 3.0 23.5 + - + +
250B THR 5.3 1.3 - - - +
251B LEU* 3.9 27.1 - - + +
254B GLN* 4.4 8.3 - - + +
278B MET 3.7 1.6 + - - -
279B LYS* 1.3 70.9 - - - +
281B MET* 1.3 61.6 + - - +
282B GLN 3.1 0.4 - - - -
283B PHE* 3.0 15.4 + - + -
284B GLN* 3.0 49.1 + - + +
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Residues in contact with MET 281 (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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29B HIS* 3.8 4.8 + - - +
246B LEU 3.0 20.6 + - - +
247B THR* 3.7 22.7 - - + -
279B LYS* 3.0 26.0 + - + +
280B VAL* 1.3 77.7 - - - +
282B GLN* 1.3 74.3 + - + +
283B PHE 3.2 0.4 - - - -
285B GLY* 3.3 9.9 + - - -
286B MET* 2.9 57.3 + - + +
287B LYS* 5.3 9.6 - - - +
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Residues in contact with GLN 282 (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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28B LYS* 6.1 0.2 - - - +
29B HIS* 3.1 20.7 + - + +
140B HIS* 3.1 49.8 + - + +
278B MET* 3.0 30.7 - - - +
279B LYS* 3.2 14.3 + - - +
280B VAL 3.1 1.6 + - - -
281B MET* 1.3 96.2 - - + +
283B PHE* 1.3 66.8 + - + +
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Residues in contact with PHE 283 (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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29B HIS* 5.1 4.6 - - - +
30B TRP 5.0 0.7 + - - +
31B VAL* 3.8 20.4 - - - +
61B ILE* 4.4 2.4 - - - +
140B HIS* 3.8 18.4 - + + -
141B VAL 3.7 12.1 - - - -
142B PHE* 3.9 12.2 - - + +
181B LYS* 3.5 29.2 - - + -
183B VAL* 3.5 31.0 - - + -
251B LEU* 3.9 28.3 - - + -
275B ILE* 4.3 7.4 - - + -
278B MET* 3.6 44.9 - - + -
279B LYS 4.1 8.3 - - - -
280B VAL* 3.0 6.8 + - + +
281B MET 3.2 1.2 - - - -
282B GLN* 1.3 84.8 - - + +
284B GLN* 1.3 63.7 + - + +
285B GLY 3.2 4.2 + - - -
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Residues in contact with GLN 284 (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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55B ILE* 4.6 11.6 - - - +
56B ILE* 3.8 21.0 - - + +
59B ASN* 3.7 20.7 + - - +
61B ILE* 3.5 11.8 - - - +
142B PHE* 4.4 17.9 - - + -
185B TYR* 4.4 9.5 - - - -
237B TRP* 3.6 27.1 - - - -
241B SER* 3.5 27.5 + - - -
246B LEU* 4.4 9.6 - - + +
254B GLN* 3.8 7.3 + - - -
280B VAL* 3.0 36.0 + - + +
283B PHE* 1.3 78.0 - - + +
285B GLY* 1.3 59.9 + - - +
286B MET* 3.7 2.0 - - + +
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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
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29B HIS* 3.7 16.9 - - - -
59B ASN* 2.9 26.2 - - - +
60B GLY 4.9 0.9 - - - +
61B ILE* 3.5 19.7 - - - +
281B MET 3.3 10.1 + - - -
283B PHE 3.2 3.4 - - - -
284B GLN* 1.3 81.1 - - - +
286B MET* 1.3 59.5 + - - +
287B LYS* 3.0 7.2 + - - +
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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