Contacts of the helix formed by residues 351 - 363 (chain F) in PDB entry 4DEM
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 351 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84F GLU* 3.8 22.4 - - + +
85F LEU* 3.8 18.4 - - + -
347F ALA* 4.9 0.2 - - - -
349F PRO 3.9 2.4 - - - +
350F LEU* 1.3 85.8 - - + +
352F PRO* 1.4 74.1 - - + +
353F ALA* 4.2 10.8 - - + +
354F VAL* 3.0 27.9 + - + +
355F PHE* 4.2 2.9 - - - -
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Residues in contact with PRO 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F ILE* 4.3 13.2 - - + -
347F ALA* 4.2 18.2 - - + -
348F ALA* 5.9 0.4 - - - +
350F LEU 3.5 7.2 - - - +
351F PRO* 1.4 80.1 - - + +
353F ALA* 1.3 58.7 + - - +
355F PHE* 2.9 7.7 + - + +
356F LEU* 2.8 42.8 + - + +
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Residues in contact with ALA 353 (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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23F VAL* 5.9 0.2 - - - +
80F VAL* 5.8 0.5 - - - +
84F GLU* 3.8 21.5 - - + +
351F PRO* 3.1 9.0 + - + +
352F PRO* 1.3 78.1 - - - +
354F VAL* 1.3 56.6 + - - +
356F LEU* 4.1 13.3 - - + +
357F GLY* 2.9 27.7 + - - -
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Residues in contact with VAL 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 5.1 1.9 + - - -
80F VAL* 5.8 2.5 - - - +
81F ALA* 4.4 8.1 - - + +
84F GLU* 3.2 35.4 + - + +
85F LEU* 4.2 14.6 - - + -
224F ILE* 3.7 36.7 - - + +
350F LEU* 5.1 4.5 - - + -
351F PRO* 3.0 30.0 + - + +
352F PRO 3.0 0.4 + - - -
353F ALA* 1.3 77.3 - - - +
355F PHE* 1.3 75.7 + - + +
357F GLY* 4.6 0.3 - - - -
358F LEU* 3.8 18.2 + - - +
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Residues in contact with PHE 355 (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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224F ILE* 4.7 2.0 - - + -
242F ALA* 4.2 12.3 - - + -
245F ILE* 3.7 32.5 - - + -
246F LEU* 4.0 35.2 - - + -
249F MET* 3.5 9.6 - - + +
343F ILE* 3.5 23.8 - - + -
346F TYR 5.4 0.4 - - - -
347F ALA* 3.9 35.2 - - + -
350F LEU* 4.0 32.8 - - + -
351F PRO 4.2 6.3 - - - -
352F PRO 2.9 4.9 + - - +
354F VAL* 1.3 86.5 - - + +
356F LEU* 1.3 65.6 + - - +
357F GLY 3.2 0.7 - - - -
358F LEU* 3.2 7.3 + - + +
359F ALA* 2.9 19.2 + - - +
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Residues in contact with LEU 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F MET* 3.6 33.3 - - + +
343F ILE* 4.0 13.0 - - + -
352F PRO* 2.8 37.4 + - + +
353F ALA* 4.1 8.1 - - + +
355F PHE* 1.3 78.2 - - - +
357F GLY* 1.3 57.1 + - - +
359F ALA* 3.3 5.4 + - - +
360F ARG* 2.9 29.6 + - - +
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Residues in contact with GLY 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 4.7 11.7 - - - -
24F TYR* 3.6 23.8 - - - -
80F VAL* 6.1 0.9 - - - -
353F ALA 2.9 16.4 + - - -
354F VAL 4.6 0.4 - - - -
356F LEU* 1.3 76.4 - - - +
358F LEU* 1.3 62.4 + - - +
360F ARG* 3.4 8.6 + - - +
361F LYS* 3.1 17.7 + - - +
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Residues in contact with LEU 358 (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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24F TYR* 3.6 18.4 - - + +
73F ASN* 6.1 3.8 - - + -
77F THR* 3.7 20.6 - - + +
219F SER 5.7 1.3 - - - +
220F PHE* 3.9 29.2 - - + +
224F ILE* 4.0 19.3 - - + -
246F LEU* 3.6 31.6 - - + -
249F MET* 4.1 10.3 - - + -
354F VAL 3.8 10.5 + - - +
355F PHE* 3.2 10.6 + - - +
357F GLY* 1.3 77.2 - - - +
359F ALA* 1.3 62.1 + - - +
361F LYS* 3.0 8.3 + - + +
362F ILE* 3.0 30.7 + - + +
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Residues in contact with ALA 359 (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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249F MET* 4.1 14.5 - - + +
336F TYR* 5.2 0.9 - - - -
339F ILE* 4.8 0.9 - - + -
340F MET* 3.3 35.7 - - + -
343F ILE* 4.7 0.9 - - + -
355F PHE 2.9 13.7 + - - +
356F LEU* 3.6 6.3 - - - +
358F LEU* 1.3 76.0 - - - +
360F ARG* 1.3 64.0 + - - +
362F ILE* 4.3 4.3 - - - -
363F TYR* 2.9 43.7 + - + +
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Residues in contact with ARG 360 (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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22F ASP 4.4 19.1 - - - +
336F TYR* 5.9 2.7 - - - -
340F MET* 5.3 0.6 - - - +
356F LEU 2.9 17.1 + - - +
357F GLY* 3.7 8.3 - - - +
358F LEU 3.3 0.2 - - - -
359F ALA* 1.3 78.9 - - - +
361F LYS* 1.3 62.9 + - + +
362F ILE 3.5 0.2 + - - -
363F TYR* 3.5 15.8 - - - +
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Residues in contact with LYS 361 (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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22F ASP 6.3 0.9 - - - +
24F TYR* 4.0 33.4 - - + -
73F ASN* 3.3 39.7 + - - +
357F GLY 3.1 13.1 + - - +
358F LEU* 3.0 15.1 + - + +
360F ARG* 1.3 79.9 - - + +
362F ILE* 1.3 64.1 + - + +
363F TYR 4.6 1.0 - - - +
365F ARG* 4.1 10.0 - - - +
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Residues in contact with ILE 362 (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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73F ASN* 5.5 7.0 - - + +
220F PHE* 3.9 33.9 - - + -
249F MET* 3.9 31.9 - - + +
252F PHE* 3.9 11.8 - - + -
253F PHE* 4.3 18.2 - - + -
256F GLN* 3.3 9.6 + - - +
358F LEU* 3.0 21.2 + - + +
359F ALA* 3.8 4.3 - - - +
361F LYS* 1.3 84.1 - - + +
363F TYR* 1.3 87.6 + - + +
365F ARG* 3.1 25.2 + - - +
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Residues in contact with TYR 363 (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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249F MET* 5.5 0.2 - - + -
252F PHE* 3.4 33.1 - + - +
332F GLU* 3.6 21.3 - - + +
335F SER* 2.7 13.6 + - - -
336F TYR* 3.6 54.3 - + + -
339F ILE* 2.5 43.8 - - + +
359F ALA* 2.9 25.9 + - + +
360F ARG* 3.5 13.8 - - - +
361F LYS 4.6 0.5 - - - +
362F ILE* 1.3 88.2 - - + +
364F LYS* 1.3 71.6 + - + +
365F ARG 3.1 4.6 + - - -
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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