Contacts of the helix formed by residues 256 - 268 (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 HIS 256 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F PRO* 4.2 23.2 - - + +
251F LEU* 3.5 13.1 + - + +
252F VAL* 5.6 0.7 - - - -
254F ASN* 3.4 40.6 + - + +
255F GLN* 1.3 76.7 + - - +
257F GLU* 1.3 63.8 + - - +
258F ASN 3.7 0.7 - - - -
259F GLU* 3.4 29.5 + - + +
260F ALA* 3.3 23.1 + - - +
286F THR 6.2 0.2 - - - -
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Residues in contact with GLU 257 (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 GLN 4.0 2.4 + - - -
256F HIS* 1.3 73.2 - - - +
258F ASN* 1.3 76.2 + - - +
259F GLU* 4.0 1.4 + - - -
260F ALA* 3.8 2.9 - - - +
261F LYS* 2.9 32.2 + - + +
286F THR* 4.5 32.2 + - + +
38H LEU* 3.7 29.9 - - - +
41H ASP* 4.1 9.9 - - - +
45H TYR* 5.0 2.4 + - - -
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Residues in contact with ASN 258 (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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257F GLU* 1.3 86.8 - - - +
259F GLU* 1.3 68.1 + - - +
261F LYS* 3.5 22.2 - - - +
262F SER* 2.9 29.8 + - - -
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Residues in contact with GLU 259 (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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211F PRO* 6.2 1.1 - - + -
212F THR* 4.1 23.8 - - + -
215F GLU* 3.5 16.3 - - - +
251F LEU* 5.3 2.7 - - + -
256F HIS* 3.4 37.1 + - + +
257F GLU 4.0 0.3 + - - -
258F ASN* 1.3 81.3 + - - +
260F ALA* 1.3 61.3 + - - +
262F SER* 3.4 5.3 + - - -
263F PHE* 2.9 29.5 + - - +
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Residues in contact with ALA 260 (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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215F GLU* 4.3 0.4 + - - -
248F TYR* 3.2 33.3 - - + +
251F LEU* 3.7 33.8 - - + +
252F VAL* 5.0 3.6 - - + +
256F HIS 3.3 19.2 + - - +
257F GLU* 3.4 3.7 + - - +
258F ASN 3.4 0.2 - - - -
259F GLU* 1.3 78.4 - - - +
261F LYS* 1.3 57.2 + - - +
263F PHE* 3.8 0.3 - - - +
264F PHE* 2.9 24.8 + - - +
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Residues in contact with LYS 261 (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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248F TYR* 4.9 3.8 + - - -
257F GLU* 2.9 21.7 + - + +
258F ASN* 3.5 24.0 - - - +
259F GLU 3.2 0.2 - - - -
260F ALA* 1.3 77.7 - - - +
262F SER* 1.3 57.6 + - - +
264F PHE* 3.8 5.3 - - - +
265F GLU* 2.9 61.7 + - + +
10H SER* 5.8 1.0 - - - +
11H ASN* 3.5 35.3 - - - +
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Residues in contact with SER 262 (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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258F ASN 2.9 17.8 + - - -
259F GLU* 3.9 4.7 - - - -
261F LYS* 1.3 76.3 - - - +
263F PHE* 1.3 58.2 + - - +
265F GLU* 3.4 9.5 + - - +
266F LYS* 2.9 31.0 + - - +
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Residues in contact with PHE 263 (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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215F GLU* 3.4 52.0 + - + +
218F TYR* 3.5 32.1 - + + -
244F PHE* 3.5 26.6 - + - -
247F MET* 4.8 13.0 - - + -
248F TYR* 5.0 3.1 - + - -
251F LEU* 3.7 23.1 - - + -
259F GLU 2.9 18.5 + - - +
260F ALA 3.9 3.1 - - - +
262F SER* 1.3 75.0 - - - +
264F PHE* 1.3 59.8 + - - +
266F LYS* 3.4 4.3 + - + +
267F PHE* 2.9 53.2 + + - +
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Residues in contact with PHE 264 (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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244F PHE* 3.9 20.9 - + - -
248F TYR* 3.6 19.7 - + + +
260F ALA 2.9 19.4 + - - +
261F LYS* 3.8 3.6 - - - +
263F PHE* 1.3 77.8 - - - +
265F GLU* 1.3 61.0 + - + +
268F HIS* 2.5 70.3 + + + +
279F LEU* 4.0 17.0 - - + -
282F LEU* 3.7 30.3 - - + -
283F SER* 3.6 35.7 - - - -
9H LEU* 4.6 11.2 - - + -
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Residues in contact with GLU 265 (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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261F LYS* 2.9 55.1 + - + +
262F SER* 3.9 8.7 - - - +
264F PHE* 1.3 82.2 - - + +
266F LYS* 1.3 59.0 + - - +
268F HIS* 3.2 25.3 - - + -
10H SER* 5.4 9.2 - - - -
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Residues in contact with LYS 266 (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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219F SER* 5.3 2.2 + - - -
262F SER* 2.9 19.1 + - - +
263F PHE* 3.9 3.1 - - + +
264F PHE 3.2 0.4 - - - -
265F GLU* 1.3 79.3 - - - +
267F PHE* 1.3 94.8 + - + +
268F HIS* 3.7 1.6 + - - -
269F GLY 4.9 1.9 + - - -
270F ASP* 4.2 4.9 - - - +
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Residues in contact with PHE 267 (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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218F TYR* 4.3 8.5 + + + -
219F SER* 3.2 34.5 - - - -
222F LYS* 3.7 27.8 - - + -
244F PHE* 3.2 34.4 - - + -
263F PHE* 2.9 39.0 + + - +
264F PHE 3.8 2.0 - - - -
266F LYS* 1.3 115.9 - - + +
268F HIS* 1.3 60.2 + - - +
269F GLY 3.7 0.4 - - - -
270F ASP* 3.3 25.9 - - - +
271F GLN* 5.5 3.1 + - - +
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Residues in contact with HIS 268 (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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244F PHE* 4.4 5.2 - - - -
264F PHE* 2.5 61.4 + + + +
265F GLU* 3.2 30.7 + - + -
266F LYS 3.7 0.8 - - - -
267F PHE* 1.3 76.9 - - - +
269F GLY* 1.3 69.9 + - - +
270F ASP 3.0 11.7 + - - -
271F GLN* 4.1 11.7 + - - +
279F LEU* 4.5 21.2 - - + +
7H LEU 3.1 27.4 + - - -
8H LYS* 3.5 23.0 - - + +
9H LEU 5.1 1.6 - - - -
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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