Contacts of the helix formed by residues 300 - 311 (chain H) 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 TYR 300 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253H TYR* 6.3 0.7 - - + -
256H LEU* 3.5 40.2 - - + -
257H PRO* 3.8 31.2 - - + +
260H SER* 4.8 15.9 - - - +
296H TYR 5.1 3.8 - - - -
297H LEU* 3.1 15.0 + - + +
298H GLU 3.1 1.2 - - - -
299H LYS* 1.3 95.3 - - + +
301H VAL* 1.3 58.4 + - - +
302H HIS* 3.1 13.0 - + - -
303H GLU* 2.9 31.6 + - - +
304H LEU* 3.8 7.2 + - + +
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Residues in contact with VAL 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H LEU* 3.2 32.5 - - + +
298H GLU* 3.0 22.1 + - - +
299H LYS 3.5 0.2 - - - -
300H TYR* 1.3 76.7 - - - +
302H HIS* 1.3 56.2 + - - +
304H LEU* 2.8 28.6 + - + +
305H ILE* 3.0 35.8 + - + +
340H ILE* 4.5 10.5 - - + -
344H PHE* 4.1 21.8 - - + -
351H ILE* 5.6 9.9 - - + -
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Residues in contact with HIS 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298H GLU 4.7 0.4 + - - -
299H LYS 3.0 28.5 + - - -
300H TYR* 3.5 14.3 - + - -
301H VAL* 1.3 78.5 - - - +
303H GLU* 1.3 81.2 + - + +
305H ILE* 4.8 3.8 - - - -
306H PRO* 3.2 21.3 - - - +
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Residues in contact with GLU 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 5.2 0.6 - - - +
260H SER* 2.6 35.0 + - - +
261H THR* 3.5 20.9 + - - +
264H SER* 3.3 25.6 + - - +
300H TYR* 2.9 13.5 + - - +
302H HIS* 1.3 106.1 + - + +
304H LEU* 1.3 65.5 + - - +
305H ILE 3.3 0.4 - - - -
306H PRO* 3.2 15.7 - - - +
307H ALA* 3.4 6.2 + - - +
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Residues in contact with LEU 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260H SER* 4.2 25.6 - - - +
263H ILE* 4.7 16.6 - - + -
286H VAL* 4.8 20.4 - - + -
289H LEU* 5.1 7.6 - - + -
290H MET* 5.7 1.8 - - + -
297H LEU* 3.7 43.1 - - + -
300H TYR* 4.0 7.2 - - + +
301H VAL* 2.8 17.4 + - + +
303H GLU* 1.3 77.6 - - - +
305H ILE* 1.3 57.7 + - + +
307H ALA* 2.9 6.5 + - + +
308H VAL* 2.4 46.9 + - + +
340H ILE* 5.7 2.7 - - + -
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Residues in contact with ILE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H VAL* 3.0 27.9 + - + +
302H HIS* 4.8 2.5 - - - -
304H LEU* 1.3 77.7 - - + +
306H PRO* 1.3 63.8 - - + +
308H VAL* 3.4 3.7 + - + +
309H MET* 2.8 49.4 + - + +
340H ILE* 3.6 46.0 - - + -
351H ILE* 5.7 7.6 - - + -
354H ARG* 6.4 1.6 - - + -
355H ILE* 4.7 19.3 - - + -
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Residues in contact with PRO 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H SER* 5.6 0.9 - - - +
302H HIS 3.2 22.9 - - - +
303H GLU* 3.2 17.5 - - - +
305H ILE* 1.3 91.1 - - + +
307H ALA* 1.3 52.9 + - - +
309H MET* 2.9 3.8 + - + -
310H THR* 2.7 44.5 + - - +
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Residues in contact with ALA 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263H ILE* 4.5 11.0 - - + -
264H SER* 4.2 17.9 - - - +
267H VAL* 4.0 26.2 - - + +
283H MET* 3.9 6.9 - - + +
286H VAL* 6.1 1.8 - - + -
303H GLU 3.4 12.1 - - - +
304H LEU* 2.9 11.3 + - - +
306H PRO* 1.3 80.3 - - - +
308H VAL* 1.3 63.4 + - + +
311H CYS* 3.2 23.0 + - - -
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Residues in contact with VAL 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET* 4.9 10.7 - - - +
286H VAL* 4.7 20.2 - - + -
304H LEU* 2.4 37.5 + - + +
305H ILE* 3.6 7.0 - - + +
307H ALA* 1.3 68.9 - - - +
309H MET* 1.3 63.9 + - + +
311H CYS* 2.9 30.0 + - - +
312H ILE* 3.5 12.2 - - + +
333H ALA* 4.6 10.2 - - + +
336H LEU* 5.4 2.9 - - + -
337H VAL* 3.6 31.2 - - + -
340H ILE* 4.0 21.3 - - + -
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Residues in contact with MET 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H ILE* 2.8 39.1 + - + +
306H PRO* 2.9 2.4 + - + +
308H VAL* 1.3 80.4 - - + +
310H THR* 1.3 60.2 + - - +
311H CYS 3.2 0.2 - - - -
312H ILE* 2.9 31.7 + - + +
313H VAL* 3.2 13.9 - - - +
337H VAL* 5.1 4.5 - - + -
355H ILE* 3.8 30.1 - - + -
358H THR* 3.8 26.7 - - + -
359H PHE* 3.6 30.1 - - + -
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Residues in contact with THR 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267H VAL* 4.7 10.1 - - + -
268H ARG* 6.2 2.9 - - + -
271H VAL* 3.9 27.7 - - + +
306H PRO* 2.7 30.8 + - - +
309H MET* 1.3 71.4 - - - +
311H CYS* 1.3 56.6 + - - +
313H VAL* 2.9 38.5 + - + +
314H SER* 3.8 7.0 + - - -
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Residues in contact with CYS 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267H VAL* 4.1 18.8 - - - -
271H VAL* 5.7 3.4 - - - -
279H LEU* 4.6 19.1 - - + -
283H MET* 3.6 28.3 - - + -
307H ALA 3.2 19.5 + - - -
308H VAL 2.9 12.2 + - - +
310H THR* 1.3 77.8 - - - +
312H ILE* 1.3 57.4 + - + +
313H VAL 3.2 3.1 + - - -
314H SER* 4.8 1.2 + - - -
327H TRP* 4.2 4.9 - - - -
330H ARG* 3.8 28.9 - - + +
333H ALA* 5.5 3.4 - - + -
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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