Contacts of the helix formed by residues 310 - 322 (chain F) in PDB entry 6MZL
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 SER 310 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F HIS* 5.0 0.5 + - - -
235F GLU* 3.4 14.6 + - - -
309F ILE* 1.3 84.7 - - - +
311F ARG* 1.3 63.5 + - - +
312F ASP* 2.5 26.1 + - - -
313F SER* 2.6 24.4 + - - -
314F TYR* 3.6 14.7 + - - +
341F ILE* 4.3 8.3 - - - +
342F PHE 3.4 17.9 - - - -
343F ASP* 3.9 7.2 - - - -
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Residues in contact with ARG 311 (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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310F SER* 1.3 71.8 - - - +
312F ASP* 1.3 61.8 + - - +
313F SER 3.2 1.6 - - - -
314F TYR* 3.1 22.9 + - - +
315F GLN* 2.9 46.7 + - - +
341F ILE* 4.5 32.6 - - + +
343F ASP* 4.1 9.8 + - - +
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Residues in contact with ASP 312 (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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231F CYS* 5.2 4.4 - - - -
232F HIS* 3.1 28.2 + - + -
310F SER* 2.5 34.1 + - - -
311F ARG* 1.3 73.2 - - - +
313F SER* 1.3 59.2 + - - -
314F TYR 3.3 0.2 - - - -
315F GLN* 3.5 22.2 - - - +
316F LEU* 2.9 33.6 + - + +
319F ARG* 5.6 1.3 - - - +
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Residues in contact with SER 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232F HIS* 4.2 14.0 + - - -
235F GLU* 4.4 5.2 + - - +
236F LEU* 3.7 38.8 - - - +
309F ILE* 4.7 4.0 - - - -
310F SER* 2.6 34.0 + - - -
311F ARG 3.2 0.4 - - - -
312F ASP* 1.3 80.2 + - - +
314F TYR* 1.3 56.7 + - - +
316F LEU* 3.4 7.1 + - - +
317F LEU* 2.9 28.2 + - - +
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Residues in contact with TYR 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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309F ILE* 5.2 10.2 - - + +
310F SER 3.6 8.5 + - - +
311F ARG* 3.1 25.3 + - - +
313F SER* 1.3 75.8 - - - +
315F GLN* 1.3 62.3 + - + +
317F LEU* 3.5 19.8 - - + +
318F LYS* 2.9 42.2 + - + +
330F TRP* 3.7 24.3 - + - -
333F VAL* 4.1 22.6 - - + +
337F LEU* 4.6 11.2 - - + -
339F ILE* 5.4 9.2 - - + -
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Residues in contact with GLN 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F ARG* 2.9 35.0 + - + +
312F ASP* 3.5 25.5 - - - +
313F SER 3.2 0.4 - - - -
314F TYR* 1.3 76.2 - - + +
316F LEU* 1.3 59.4 + - - +
318F LYS* 3.3 5.6 + - - +
319F ARG* 2.9 60.1 + - - +
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Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F PHE* 4.4 20.8 - - + -
228F SER* 4.7 11.2 - - - +
232F HIS* 3.5 42.2 - - + +
236F LEU* 5.9 3.8 - - + -
312F ASP* 2.9 16.6 + - + +
313F SER* 3.7 6.1 - - - +
315F GLN* 1.3 75.9 - - - +
317F LEU* 1.3 56.8 + - - +
319F ARG* 3.4 25.1 - - + +
320F HIS* 2.9 32.2 + - - +
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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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221F LEU* 5.0 16.2 - - + -
225F ILE* 6.1 2.5 - - + -
236F LEU* 6.5 0.7 - - + -
239F LEU* 5.3 16.4 - - + -
309F ILE* 6.5 1.3 - - + -
313F SER 2.9 17.3 + - - +
314F TYR* 3.5 29.6 - - + +
315F GLN 3.2 0.2 - - - -
316F LEU* 1.3 76.8 - - - +
318F LYS* 1.3 56.4 + - - +
320F HIS* 3.4 2.5 + - + -
321F LEU* 2.9 62.0 + - + +
329F ILE* 5.5 1.6 - - + -
330F TRP* 5.6 1.1 - - + -
333F VAL* 3.8 24.0 - - + -
337F LEU* 5.1 6.5 - - + -
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Residues in contact with LYS 318 (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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314F TYR* 2.9 35.8 + - + +
315F GLN* 3.8 5.6 - - - +
317F LEU* 1.3 76.0 - - - +
319F ARG* 1.3 60.7 + - + +
321F LEU* 3.8 3.1 - - - -
322F GLN* 3.0 65.1 + - + +
330F TRP* 5.0 17.9 - - + -
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Residues in contact with ARG 319 (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 PHE* 6.0 0.9 - - + -
312F ASP* 4.4 2.2 + - - +
315F GLN* 2.9 48.2 + - - +
316F LEU* 3.4 42.1 - - + +
317F LEU 3.4 0.2 - - - -
318F LYS* 1.3 77.1 - - + +
320F HIS* 1.3 60.7 + - - +
322F GLN* 4.3 11.2 + - - +
323F GLU* 4.2 14.9 + - - +
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Residues in contact with HIS 320 (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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220F GLY 4.6 3.5 + - - -
221F LEU* 3.5 34.2 + - + +
224F PHE* 3.6 51.1 - + + +
316F LEU 2.9 17.7 + - - +
317F LEU* 4.0 4.0 - - + +
319F ARG* 1.3 77.9 - - - +
321F LEU* 1.3 68.8 + - + +
322F GLN 3.3 0.9 - - - -
323F GLU* 3.2 44.9 + - - +
324F LYS* 4.0 22.2 + - - +
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Residues in contact with LEU 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F LEU* 4.7 6.3 - - + -
317F LEU* 2.9 42.8 + - + +
318F LYS 4.5 0.9 - - - +
320F HIS* 1.3 84.2 - - + +
322F GLN* 1.3 63.1 + - - +
323F GLU 3.2 1.1 - - - -
324F LYS* 3.2 36.2 + - + +
327F ASN* 3.4 28.3 + - - +
329F ILE* 4.1 20.2 - - + -
330F TRP* 3.8 34.6 - - + +
333F VAL* 3.9 12.3 - - + -
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Residues in contact with GLN 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LYS* 3.0 55.4 + - + +
319F ARG* 4.7 9.5 - - - +
320F HIS 3.3 0.6 - - - -
321F LEU* 1.3 75.8 - - - +
323F GLU* 1.3 62.2 + - - +
324F LYS 3.2 0.8 + - - -
325F GLN* 3.7 17.2 + - - +
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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