Contacts of the helix formed by residues 279 - 290 (chain F) in PDB entry 4NFI
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 THR 279 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277F ARG 3.6 2.0 + - - +
278F ALA* 1.3 73.5 - - - +
280F PRO* 1.3 70.7 - - + +
281F GLU* 3.4 9.2 + - - +
282F GLN* 2.8 42.9 + - - +
283F TYR* 2.8 28.0 + - - +
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Residues in contact with PRO 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F ALA 4.6 1.1 - - - +
279F THR* 1.3 86.9 - - + +
281F GLU* 1.3 61.3 + - - +
283F TYR* 3.4 11.8 + - + +
284F GLN* 3.1 22.7 + - - +
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F THR* 3.1 9.4 + - - +
280F PRO* 1.3 78.1 - - - +
282F GLN* 1.3 64.2 + - + +
284F GLN* 3.1 17.7 + - + +
285F ILE* 3.2 27.4 + - + +
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Residues in contact with GLN 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ARG 4.2 0.5 - - - +
278F ALA* 3.4 16.5 - - + -
279F THR* 2.8 40.9 + - - +
281F GLU* 1.3 77.4 - - + +
283F TYR* 1.3 59.6 + - - +
285F ILE* 3.2 15.4 + - + +
286F LEU* 2.9 29.6 + - - +
304F LEU* 3.5 21.7 - - + +
307F GLU* 3.5 29.5 + - - +
308F LEU* 3.5 26.5 - - - +
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Residues in contact with TYR 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F ASP* 5.2 1.0 + - - -
185F LEU* 3.6 33.3 + - + +
186F VAL* 4.5 14.4 - - + +
275F LEU* 3.6 26.5 - - + -
278F ALA* 3.9 10.6 - - + +
279F THR 2.8 13.1 + - - +
280F PRO* 3.4 14.8 - - + +
282F GLN* 1.3 77.0 - - - +
284F GLN* 1.3 65.1 + - - +
286F LEU* 3.3 7.6 + - - +
287F LYS* 2.9 52.0 + - + +
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Residues in contact with GLN 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F PRO 3.1 11.7 + - - +
281F GLU* 3.1 13.1 + - - +
283F TYR* 1.3 82.4 - - - +
285F ILE* 1.3 66.3 + - + +
287F LYS* 3.2 34.8 + - - +
288F GLU* 2.9 53.4 + - - +
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Residues in contact with ILE 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F GLU* 3.2 30.7 + - + +
282F GLN* 3.2 20.3 + - + +
284F GLN* 1.3 77.0 - - + +
286F LEU* 1.3 62.5 + - - +
288F GLU* 3.3 8.3 + - - +
289F ASN* 2.8 35.6 + - + +
300F ARG* 3.5 57.0 - - + +
301F VAL* 6.1 0.4 - - - -
304F LEU* 4.5 11.0 - - + -
307F GLU* 5.8 0.7 - - - +
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Residues in contact with LEU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F LEU* 3.9 13.0 - - + -
271F VAL* 4.0 14.4 - - + -
274F CYS* 3.9 27.4 - - - -
275F LEU* 3.8 29.8 - - + -
278F ALA* 5.9 0.7 - - + -
282F GLN 2.9 13.0 + - - +
283F TYR* 3.4 11.0 - - - +
285F ILE* 1.3 76.8 - - - +
287F LYS* 1.3 57.9 + - - +
289F ASN* 3.2 2.5 + - - -
290F TYR* 2.8 57.1 + - + +
301F VAL* 4.1 21.1 - - + +
304F LEU* 4.0 9.3 - - + +
305F TYR* 4.3 3.6 - - + -
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Residues in contact with LYS 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 3.7 31.2 - - + +
185F LEU* 3.7 15.2 - - + +
283F TYR* 2.9 41.3 + - + +
284F GLN* 3.2 36.6 - - - +
286F LEU* 1.3 79.7 - - - +
288F GLU* 1.3 59.9 + - - +
289F ASN 3.4 0.2 + - - -
290F TYR 4.0 3.3 + - - -
292F GLN* 4.4 4.2 + - - -
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Residues in contact with GLU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F GLN* 2.9 48.6 + - - +
285F ILE* 4.3 9.9 - - - +
286F LEU 3.3 0.4 - - - -
287F LYS* 1.3 73.4 - - + +
289F ASN* 1.3 70.3 + - - +
292F GLN* 2.8 19.4 + - - +
297F LYS* 4.2 5.9 + - - +
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Residues in contact with ASN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ILE* 4.6 2.3 - - - +
285F ILE* 2.8 31.9 + - - +
288F GLU* 1.3 92.4 + - - +
290F TYR* 1.3 61.9 + - - +
291F GLY 4.0 0.3 + - - -
292F GLN* 3.6 9.4 + - - +
297F LYS* 3.4 56.0 + - - +
298F VAL 4.4 0.3 + - - -
300F ARG* 3.9 24.5 - - + +
301F VAL* 3.7 15.7 - - + +
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Residues in contact with TYR 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 3.3 20.5 - - + +
185F LEU* 4.5 9.0 - - + -
188F PHE* 3.6 18.8 - + - -
261F ASP* 3.8 6.4 + - - +
262F ILE* 3.9 33.1 - - + +
265F ASN* 3.3 33.0 - - - -
266F LYS 2.7 30.9 + - - -
268F SER* 4.0 6.6 + - - -
271F VAL* 3.7 14.8 - - + +
286F LEU* 2.8 38.9 + - + +
287F LYS 4.0 1.0 + - - +
288F GLU 3.8 0.2 - - - -
289F ASN* 1.3 71.6 - - - +
291F GLY* 1.3 68.0 + - - +
292F GLN* 3.1 15.8 + - - +
301F VAL* 4.2 4.0 - - + -
305F TYR* 3.5 18.7 + - - -
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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