Contacts of the helix formed by residues 330 - 340 (chain F) in PDB entry 3HX0
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 330 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328F ILE 3.3 2.7 + - - -
329F SER* 1.3 74.1 + - - +
331F SER* 1.3 64.9 + - - +
333F PRO* 3.2 17.4 - - - +
334F VAL* 4.3 8.3 - - - +
353F TYR* 4.2 10.7 + - - +
358F ARG* 5.3 5.7 + - - -
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Residues in contact with SER 331 (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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270F GLN* 4.8 3.6 + - - -
329F SER* 2.8 23.1 + - - -
330F GLU* 1.3 81.9 - - - +
332F VAL* 1.3 74.3 + - - +
334F VAL* 2.9 16.5 + - - +
335F LEU* 2.9 24.1 + - - +
353F TYR* 3.0 40.6 - - - -
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Residues in contact with VAL 332 (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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266F ALA* 3.9 25.1 - - + +
269F VAL* 3.9 8.2 - - + +
270F GLN* 4.0 28.9 - - + +
328F ILE* 3.4 22.9 - - + -
329F SER* 3.4 16.2 - - - +
331F SER* 1.3 75.5 + - - +
333F PRO* 1.3 60.3 - - + +
335F LEU* 3.6 9.1 - - - +
336F GLU* 2.7 54.4 + - - +
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Residues in contact with PRO 333 (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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328F ILE* 5.2 2.7 - - + +
329F SER 3.5 7.0 - - - +
330F GLU* 3.2 19.7 - - - +
332F VAL* 1.3 96.9 - - + +
334F VAL* 1.3 59.1 + - + +
336F GLU* 3.4 9.9 + - + +
337F LEU* 2.9 28.8 + - - +
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Residues in contact with VAL 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F GLU 4.3 9.9 - - - +
331F SER 2.9 8.1 + - - +
333F PRO* 1.3 77.5 - - + +
335F LEU* 1.3 63.2 + - - +
337F LEU* 3.2 10.4 + - + +
338F PHE* 3.1 46.1 + - + -
353F TYR* 3.8 17.3 - - + +
358F ARG* 3.2 48.0 - - + +
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Residues in contact with LEU 335 (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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269F VAL* 4.8 24.5 - - + +
270F GLN* 5.0 9.9 - - + -
331F SER* 2.9 34.8 + - - +
332F VAL* 3.6 9.2 - - - +
334F VAL* 1.3 75.3 - - - +
336F GLU* 1.3 63.8 + - - +
338F PHE* 3.1 6.5 + - - +
339F SER* 3.0 25.8 + - - -
349F ALA* 3.6 34.7 - - + +
350F GLN* 4.1 12.6 - - + +
353F TYR* 3.6 28.5 - - + -
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Residues in contact with GLU 336 (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 VAL 5.5 0.7 - - - +
265F LYS* 3.3 31.3 - - - +
266F ALA* 5.0 0.5 + - - -
269F VAL* 4.0 25.0 - - + +
332F VAL* 2.7 39.3 + - - +
333F PRO* 3.6 8.2 - - + +
335F LEU* 1.3 72.0 - - - +
337F LEU* 1.3 59.1 + - - +
339F SER* 3.5 4.2 + - - -
340F ASN* 2.9 37.2 + - - +
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Residues in contact with LEU 337 (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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333F PRO 2.9 14.3 + - - +
334F VAL* 3.2 11.0 - - - +
335F LEU 3.1 0.2 - - - -
336F GLU* 1.3 77.3 - - - +
338F PHE* 1.3 72.7 + - + +
340F ASN* 3.2 15.7 + - - +
341F ILE* 4.1 0.7 - - - +
358F ARG 4.6 4.3 - - - +
359F SER* 4.2 7.2 - - - -
360F LEU* 3.6 42.6 - - + +
380F TYR* 2.9 53.8 + - + +
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Residues in contact with PHE 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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334F VAL* 3.1 40.0 + - + -
335F LEU* 3.1 6.5 + - - +
337F LEU* 1.3 85.9 - - + +
339F SER* 1.3 59.2 + - - +
341F ILE* 2.9 32.9 - - - +
344F ALA* 3.6 7.1 - - - +
349F ALA* 3.8 25.6 - - + -
352F TRP* 3.7 39.3 - + + -
353F TYR* 4.2 5.6 - + - -
357F PHE* 3.9 15.0 - - + -
358F ARG 3.8 10.1 - - - -
359F SER* 3.9 15.9 - - - -
360F LEU* 4.2 3.4 - - + -
363F ILE* 3.6 26.7 - - + -
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Residues in contact with SER 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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269F VAL* 4.7 12.4 - - - +
335F LEU 3.0 14.1 + - - -
336F GLU* 3.7 12.8 - - - -
337F LEU 3.2 0.2 - - - -
338F PHE* 1.3 72.5 - - - +
340F ASN* 1.3 56.8 + - - +
341F ILE 2.8 6.1 + - - -
344F ALA 3.2 13.0 - - - +
345F GLY* 4.3 8.9 - - - -
346F THR* 4.4 3.3 + - - -
349F ALA* 3.5 14.5 - - - +
806F NA 2.3 31.5 - - - -
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Residues in contact with ASN 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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336F GLU* 2.9 30.3 + - - +
337F LEU* 3.2 3.6 + - - +
339F SER* 1.3 75.9 - - - +
341F ILE* 1.3 57.4 + - - +
342F TRP 3.6 2.8 + - - -
376F GLY 5.1 0.9 - - - +
380F TYR* 3.3 43.2 + - + +
383F PHE* 5.5 6.6 - - - +
384F LEU* 4.1 21.0 - - + +
806F NA 4.2 0.2 - - - -
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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