Contacts of the helix formed by residues 294 - 308 (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 GLU 294 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F GLN* 3.3 18.3 - - - +
293F LYS* 1.3 98.0 + - + +
295F ALA* 1.4 65.1 + - - +
296F GLU* 3.5 19.5 - - - +
297F LYS* 3.0 50.0 + - + +
298F VAL* 3.1 12.7 + - - +
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Residues in contact with ALA 295 (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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263F GLN* 6.1 0.4 - - - +
293F LYS 3.2 6.4 + - - +
294F GLU* 1.4 70.8 - - - +
296F GLU* 1.3 60.7 + - - +
298F VAL* 3.4 8.9 + - - +
299F ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLU* 3.5 25.2 - - - +
295F ALA* 1.3 76.1 + - - +
297F LYS* 1.3 71.0 + - + +
299F ALA* 3.7 8.5 - - + +
300F ARG* 3.2 24.1 + - - +
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Residues in contact with LYS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F GLU 4.2 4.9 + - - +
289F ASN* 3.4 37.1 + - - +
292F GLN* 3.3 37.9 + - + +
294F GLU* 3.0 45.9 + - + +
296F GLU* 1.3 87.9 + - + +
298F VAL* 1.3 64.5 + - - +
300F ARG* 3.1 12.0 + - - +
301F VAL* 3.2 17.7 + - - +
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Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LEU* 5.1 7.2 - - + -
262F ILE* 4.0 33.4 - - + +
263F GLN* 3.5 46.9 - - + +
289F ASN 5.5 0.2 - - - +
292F GLN 3.7 8.3 - - - +
293F LYS 4.7 0.4 - - - +
294F GLU 3.1 14.6 + - - +
295F ALA* 3.7 9.4 - - - +
297F LYS* 1.3 75.5 - - - +
299F ALA* 1.3 62.6 + - - +
301F VAL* 3.2 5.2 + - - +
302F LYS* 3.0 20.7 + - + +
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Residues in contact with ALA 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ALA 3.0 17.8 + - - +
296F GLU* 3.8 9.4 - - - +
297F LYS 3.2 0.4 - - - -
298F VAL* 1.3 76.9 - - - +
300F ARG* 1.3 56.8 + - - +
302F LYS* 3.4 9.3 + - - +
303F ALA* 3.0 28.1 + - - +
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Residues in contact with ARG 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F ILE* 3.5 47.4 - - + +
289F ASN* 3.9 17.9 - - - +
296F GLU 3.2 13.1 + - - +
297F LYS 3.1 9.9 + - - +
299F ALA* 1.3 74.4 - - - +
301F VAL* 1.3 60.2 + - - +
303F ALA* 3.4 12.0 + - - +
304F LEU* 3.0 34.1 + - - +
307F GLU* 4.5 11.3 + - - -
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Residues in contact with VAL 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F ILE* 3.8 25.4 - - + -
285F ILE* 6.1 1.1 - - + -
286F LEU* 4.1 15.9 - - + +
289F ASN* 3.7 31.0 - - + +
290F TYR* 4.1 8.1 - - + +
297F LYS 3.2 13.4 + - - +
298F VAL 3.2 7.4 + - - +
300F ARG* 1.3 77.4 - - - +
302F LYS* 1.3 63.3 + - - +
304F LEU* 3.1 9.3 + - - +
305F TYR* 3.0 54.0 + - + +
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Residues in contact with LYS 302 (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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248F LEU* 3.5 55.1 + - + +
249F PHE* 4.0 16.7 - - + +
262F ILE* 4.6 0.6 - - - +
298F VAL* 3.0 12.9 + - + +
299F ALA* 3.6 12.3 - - - +
301F VAL* 1.3 77.8 - - - +
303F ALA* 1.3 56.2 + - - +
305F TYR* 3.3 3.4 + - - +
306F GLU* 2.9 52.7 + - - +
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Residues in contact with ALA 303 (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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299F ALA 3.0 17.5 + - - +
300F ARG* 3.6 18.2 - - - +
302F LYS* 1.3 75.0 - - - +
304F LEU* 1.3 57.8 + - - +
306F GLU* 3.3 14.3 + - - +
307F GLU* 2.8 30.3 + - - +
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Residues in contact with LEU 304 (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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274F CYS* 3.8 25.6 - - - -
282F GLN* 3.5 50.0 - - + +
285F ILE* 4.5 8.7 - - + -
286F LEU* 4.0 19.5 - - + +
300F ARG* 3.0 23.3 + - - +
301F VAL* 3.1 10.5 + - - +
303F ALA* 1.3 76.8 - - - +
305F TYR* 1.3 61.6 + - + +
307F GLU* 3.2 20.6 + - - +
308F LEU* 3.0 29.8 + - + +
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Residues in contact with TYR 305 (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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248F LEU* 3.3 31.0 - - + -
249F PHE* 4.1 10.5 - - + -
262F ILE* 4.5 5.3 - - + +
268F SER* 4.4 0.9 + - - -
270F LEU* 3.4 30.0 - - + +
271F VAL* 3.3 26.0 + - - +
274F CYS* 3.6 31.9 - - + -
286F LEU* 4.3 3.1 - - + -
290F TYR* 3.5 17.7 + - - -
301F VAL* 3.0 32.2 + - + -
302F LYS 3.5 6.7 - - - +
304F LEU* 1.3 76.2 - - + +
306F GLU* 1.3 60.8 + - - +
308F LEU* 3.3 1.9 + - - -
309F ASP 3.2 4.0 + - - -
310F LEU* 3.1 48.0 + - + +
311F PRO* 4.6 1.3 - - - -
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Residues in contact with GLU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F PHE* 3.7 21.2 - - + -
302F LYS* 2.9 45.7 + - - +
303F ALA* 3.6 12.5 - - - +
305F TYR* 1.3 72.2 - - - +
307F GLU* 1.3 66.4 + - - +
309F ASP* 3.1 14.1 + - - +
311F PRO* 4.5 10.1 - - + -
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Residues in contact with GLU 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F GLN* 3.5 28.2 + - - +
285F ILE* 5.8 0.7 - - - +
300F ARG* 4.5 12.1 + - - -
303F ALA 2.8 15.9 + - - +
304F LEU* 3.2 20.8 + - - +
306F GLU* 1.3 78.0 - - - +
308F LEU* 1.3 59.0 + - - +
309F ASP* 3.3 3.7 + - - +
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Residues in contact with LEU 308 (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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274F CYS* 3.7 43.1 - - + +
277F ARG* 4.2 29.4 + - + +
278F ALA* 4.5 3.6 - - + -
282F GLN* 3.5 34.8 - - - +
304F LEU* 3.0 27.2 + - + +
305F TYR* 3.3 4.2 + - - +
306F GLU 3.1 0.4 - - - -
307F GLU* 1.3 76.8 - - + +
309F ASP* 1.3 68.7 + - - +
310F LEU* 3.2 18.6 + - + +
313F VAL* 4.6 1.6 - - - +
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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