Contacts of the helix formed by residues 337 - 349 (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 PRO 337 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70F GLU* 3.7 22.4 - - + +
71F LEU* 3.8 19.1 - - + -
335F PRO 4.5 2.2 - - - +
336F LEU* 1.3 88.4 - - + +
338F PRO* 1.4 73.0 - - + +
339F ALA* 4.3 9.9 - - + +
340F VAL* 3.0 27.4 + - + +
341F PHE* 4.3 2.1 + - - -
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Residues in contact with PRO 338 (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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329F ILE* 4.3 14.4 - - + +
333F ALA* 4.3 17.5 - - + -
336F LEU 3.4 8.7 - - - +
337F PRO* 1.4 80.9 - - + +
339F ALA* 1.3 56.9 + - - +
341F PHE* 2.9 24.2 + - + +
342F LEU* 3.0 27.1 + - + +
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Residues in contact with ALA 339 (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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66F VAL* 5.8 0.5 - - - +
70F GLU* 3.5 23.1 - - + +
337F PRO* 3.1 8.8 - - + +
338F PRO* 1.3 78.3 - - - +
340F VAL* 1.3 62.2 + - - +
342F LEU* 3.7 15.1 - - + +
343F GLY* 3.0 21.8 + - - -
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Residues in contact with VAL 340 (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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10F TYR* 5.2 1.2 + - - -
63F THR* 5.8 0.2 - - - +
66F VAL* 5.7 3.6 - - - +
67F ALA* 4.2 11.0 - - + +
70F GLU* 3.2 32.1 + - + +
71F LEU* 4.0 27.8 - - + -
210F ILE* 3.7 39.1 - - + +
336F LEU* 5.1 3.6 - - + -
337F PRO* 3.0 21.2 + - + +
339F ALA* 1.3 77.5 - - - +
341F PHE* 1.3 73.3 + - + +
343F GLY* 4.6 0.3 - - - -
344F LEU* 3.9 15.4 + - - +
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Residues in contact with PHE 341 (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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210F ILE* 4.7 6.3 - - + -
228F ALA* 4.1 18.6 - - + -
231F ILE* 3.6 40.6 - - + -
232F LEU* 4.0 34.8 - - + -
235F MET* 3.4 12.4 - - + +
329F ILE* 3.6 23.3 - - + -
332F TYR 5.3 0.7 - - - -
333F ALA* 3.9 34.1 - - + -
336F LEU* 4.2 21.1 - - + -
337F PRO 4.4 3.4 - - - -
338F PRO 2.9 9.3 + - - +
340F VAL* 1.3 83.1 - - + +
342F LEU* 1.3 59.2 + - - +
343F GLY 3.3 0.2 - - - -
344F LEU* 3.4 4.9 + - - +
345F ALA* 2.9 24.1 + - - +
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Residues in contact with LEU 342 (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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326F MET* 3.6 32.5 - - + +
329F ILE* 4.1 11.7 - - + -
338F PRO* 3.0 36.0 + - + +
339F ALA* 4.1 9.4 - - + +
341F PHE* 1.3 77.3 - - - +
343F GLY* 1.3 56.8 + - - +
345F ALA* 3.8 4.2 - - - +
346F ARG* 3.0 30.3 + - - +
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Residues in contact with GLY 343 (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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8F ASP* 5.4 0.3 - - - +
9F VAL* 4.7 12.1 - - - -
10F TYR* 3.4 22.8 - - - -
66F VAL* 6.0 1.3 - - - -
339F ALA 3.0 16.5 + - - -
340F VAL 4.6 0.4 - - - -
342F LEU* 1.3 75.8 - - - +
344F LEU* 1.3 61.7 + - - +
346F ARG* 3.5 6.5 + - - +
347F LYS* 3.1 18.5 + - - +
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Residues in contact with LEU 344 (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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10F TYR* 3.5 14.2 + - + +
59F ASN* 5.2 4.5 - - + +
63F THR* 3.4 38.4 - - + +
205F SER 5.5 3.1 - - - +
206F PHE* 3.8 34.8 - - + +
209F PRO* 6.4 0.2 - - + -
210F ILE* 4.2 7.0 - - + -
232F LEU* 3.8 29.8 - - + -
235F MET* 4.0 5.2 - - + -
340F VAL 3.9 10.1 + - - +
341F PHE* 3.4 8.5 + - - +
342F LEU 3.4 0.2 - - - -
343F GLY* 1.3 76.7 - - - +
345F ALA* 1.3 61.0 + - - +
347F LYS* 3.2 8.3 + - + +
348F ILE* 3.1 29.9 + - + +
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Residues in contact with ALA 345 (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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235F MET* 3.8 16.0 - - + +
322F TYR* 5.0 0.2 - - - -
325F ILE* 4.7 0.9 - - + -
326F MET* 3.3 34.3 - - + -
341F PHE 2.9 20.7 + - - +
342F LEU* 3.4 2.7 + - - +
344F LEU* 1.3 70.9 - - - +
346F ARG* 1.3 58.4 + - - +
348F ILE* 3.0 9.3 + - - -
349F TYR* 2.8 44.3 + - + +
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Residues in contact with ARG 346 (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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8F ASP* 4.7 13.7 - - + +
322F TYR* 5.7 3.8 - - - -
326F MET* 5.2 0.6 - - - +
342F LEU 3.0 17.6 + - - +
343F GLY* 3.8 7.0 - - - +
345F ALA* 1.3 75.0 - - - +
347F LYS* 1.3 62.2 + - + +
349F TYR* 3.6 15.2 - - - +
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Residues in contact with LYS 347 (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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8F ASP* 3.5 32.9 + - - +
10F TYR* 3.5 42.2 - - + +
59F ASN* 3.6 34.3 + - + +
343F GLY 3.1 11.8 + - - +
344F LEU* 3.4 11.0 - - + +
345F ALA 3.2 0.4 - - - -
346F ARG* 1.3 79.8 - - + +
348F ILE* 1.3 65.7 + - + +
349F TYR 4.6 0.5 - - - +
351F ARG* 3.9 12.5 - - - +
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Residues in contact with ILE 348 (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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59F ASN* 6.1 1.8 - - + +
206F PHE* 4.0 27.6 - - + -
235F MET* 4.0 29.6 - - + +
238F PHE* 3.9 15.9 - - + -
239F PHE* 4.2 18.6 - - + -
242F GLN* 3.1 18.7 + - - +
344F LEU* 3.1 16.5 + - + +
345F ALA* 3.0 6.8 + - - +
347F LYS* 1.3 82.8 - - + +
349F TYR* 1.3 93.5 + - + +
351F ARG* 3.1 20.8 + - - +
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Residues in contact with TYR 349 (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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235F MET* 4.8 0.6 - - + -
238F PHE* 3.2 42.8 - + - +
318F GLU* 3.7 11.9 - - + -
321F SER* 2.7 21.1 + - - -
322F TYR* 3.5 57.9 - + + -
325F ILE* 3.1 25.2 - - + +
345F ALA* 2.8 34.6 + - + +
346F ARG* 3.6 14.2 - - - +
347F LYS 4.6 0.3 - - - +
348F ILE* 1.3 97.2 - - + +
350F LYS* 1.3 73.5 + - + +
351F ARG 3.5 0.9 + - - -
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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