Contacts of the helix formed by residues 306 - 320 (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 GLY 306 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300F CYS* 4.6 3.8 - - - -
305F ILE* 1.3 74.8 - - - +
307F LYS* 1.3 68.0 + - - -
308F ARG 3.1 2.9 - - - -
309F MET 2.8 13.9 + - - -
310F ALA* 2.8 14.2 + - - -
2I C 3.0 21.6 + - - -
3I C 4.5 8.5 - - - -
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Residues in contact with LYS 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F TYR* 3.2 22.0 + - - +
300F CYS* 4.4 6.2 - - - -
306F GLY* 1.3 67.9 - - - -
308F ARG* 1.3 56.6 + - + +
310F ALA* 4.3 1.8 - - - -
311F GLU* 2.8 44.6 + - - +
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Residues in contact with ARG 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F GLY 2.9 3.6 + - - -
307F LYS* 1.3 79.1 - - + +
309F MET* 1.3 61.7 + - - +
311F GLU* 3.4 16.4 + - - +
312F LYS* 3.4 20.2 + - - +
1I G 3.5 43.2 + - - -
2I C 3.4 23.8 + - - +
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Residues in contact with MET 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F LEU* 4.1 31.6 - - + -
278F GLY 4.7 1.1 - - - +
279F TYR* 3.6 47.1 - - + +
282F ALA* 3.6 31.0 - - + -
286F LEU* 6.4 0.2 - - + -
305F ILE* 3.6 19.7 - - + -
306F GLY 2.8 8.8 + - - +
308F ARG* 1.3 74.1 - - - +
310F ALA* 1.3 58.9 + - - +
312F LYS* 2.8 30.6 + - - +
313F ILE* 3.1 14.9 + - + +
1I G 4.1 12.5 + - - +
2I C 3.1 16.7 + - - +
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Residues in contact with ALA 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F TYR* 3.3 30.8 - - + -
299F ALA* 3.9 15.4 - - + +
300F CYS* 3.5 23.8 - - - -
305F ILE* 3.8 4.1 - - + +
306F GLY 2.8 16.2 + - - +
307F LYS 3.7 0.7 - - - +
309F MET* 1.3 72.5 - - - +
311F GLU* 1.3 63.2 + - - +
313F ILE* 3.0 20.8 + - - +
314F ILE* 3.1 11.8 + - - +
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Residues in contact with GLU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F TYR* 3.9 17.1 + - + +
307F LYS* 2.8 35.5 + - - +
308F ARG* 3.5 11.7 + - - +
309F MET 3.2 0.2 - - - -
310F ALA* 1.3 75.6 - - - +
312F LYS* 1.3 59.5 + - + +
314F ILE* 4.4 3.7 - - - +
315F GLU* 3.7 21.1 + - - +
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Residues in contact with LYS 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F LEU* 4.5 16.8 - - + -
263F LEU* 4.2 20.0 - - + -
267F TYR* 5.8 0.2 - - - -
279F TYR* 3.3 21.2 + - - +
308F ARG* 3.4 21.2 + - - +
309F MET* 2.8 15.4 + - - +
311F GLU* 1.3 80.6 - - + +
313F ILE* 1.3 62.5 + - - +
314F ILE 3.4 0.2 - - - -
315F GLU* 3.5 8.2 + - - +
316F ILE* 3.2 28.9 + - - +
322F LEU* 4.3 17.7 - - + +
324F LYS* 5.0 8.1 - - + -
1I G 2.7 31.8 - - - -
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Residues in contact with ILE 313 (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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256F ILE* 3.8 36.3 - - + -
260F LEU* 5.0 4.7 - - + -
286F LEU* 4.4 16.4 - - + -
293F VAL* 4.8 4.0 - - + -
299F ALA* 3.6 30.5 - - + -
305F ILE* 4.1 28.5 - - + -
309F MET* 3.1 15.2 + - + +
310F ALA* 3.0 6.5 + - - +
312F LYS* 1.3 75.5 - - + +
314F ILE* 1.3 61.1 + - + +
316F ILE* 3.0 8.2 + - - +
317F LEU* 2.8 40.4 + - + +
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Residues in contact with ILE 314 (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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294F THR 4.7 2.0 - - - +
295F SER* 3.8 7.9 - - - -
296F TYR* 3.1 61.9 - - + +
310F ALA 3.1 5.2 + - - +
311F GLU* 4.6 3.8 - - - +
313F ILE* 1.3 77.1 - - + +
315F GLU* 1.3 60.1 + - - +
316F ILE 3.0 0.2 + - - -
317F LEU* 3.0 14.3 + - + +
318F GLU* 2.8 63.7 + - + +
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Residues in contact with GLU 315 (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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311F GLU 3.7 15.3 + - - +
312F LYS* 3.5 10.8 + - - +
313F ILE 3.3 0.4 - - - -
314F ILE* 1.3 80.1 - - - +
316F ILE* 1.3 56.0 + - - +
318F GLU* 5.2 2.2 - - - -
319F SER* 2.9 39.2 + - - +
321F HIS 3.2 9.7 - - - +
322F LEU* 3.7 18.2 - - + +
323F ARG* 3.0 35.1 + - - +
324F LYS 5.4 0.3 + - - -
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Residues in contact with ILE 316 (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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255F HIS* 3.7 25.6 - - + +
256F ILE* 4.3 22.2 - - + +
259F LYS* 3.7 42.4 - - + -
260F LEU* 4.6 11.4 - - + -
312F LYS 3.2 15.4 + - - +
313F ILE* 3.0 9.3 + - - +
314F ILE 3.0 0.8 - - - -
315F GLU* 1.3 79.3 - - - +
317F LEU* 1.3 59.7 + - - +
318F GLU 3.4 0.2 - - - -
320F GLY* 2.7 30.4 + - - +
321F HIS 4.1 5.6 - - - +
322F LEU* 4.2 21.8 - - + -
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Residues in contact with LEU 317 (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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255F HIS* 3.4 35.7 - - + +
256F ILE* 3.9 8.3 - - + -
293F VAL* 3.1 27.4 - - + +
294F THR* 3.8 23.1 - - - +
295F SER* 4.6 1.1 - - - +
313F ILE* 2.8 33.4 + - + +
314F ILE* 3.0 14.1 + - + +
316F ILE* 1.3 78.6 - - - +
318F GLU* 1.3 64.1 + - + +
320F GLY 4.6 0.9 + - - -
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Residues in contact with GLU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F ILE* 2.8 43.7 + - + +
315F GLU* 5.0 1.9 - - - +
317F LEU* 1.3 81.3 - - + +
319F SER* 1.3 64.8 + - - +
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Residues in contact with SER 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F GLU* 2.9 26.9 + - - +
318F GLU* 1.3 81.4 + - - +
320F GLY* 1.3 59.0 + - - +
321F HIS* 2.9 22.3 + - - +
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Residues in contact with GLY 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F LYS* 3.3 22.0 + - - -
316F ILE* 2.7 27.8 + - - -
317F LEU 4.5 1.2 + - - -
318F GLU 3.8 0.6 - - - -
319F SER* 1.3 71.3 - - - +
321F HIS* 1.3 58.2 + - - +
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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