Contacts of the helix formed by residues 269 - 277 (chain T) 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 ARG 269 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113P PHE* 3.3 37.4 - - - -
118P LEU* 3.4 51.2 - - + +
121P TYR* 6.4 2.2 - - + -
122P GLU* 3.3 15.7 - - + +
268T ILE* 1.3 74.3 - - - +
270T LEU* 1.3 62.8 + - - +
271T GLU 3.5 0.7 - - - +
272T GLY* 4.3 20.2 - - - +
273T LEU* 3.3 19.1 + - - +
334T GLY 3.3 12.3 + - - -
335T PHE* 3.0 57.2 + - + +
336T ARG 5.7 0.2 - - - -
337T LYS* 6.2 1.3 - - + -
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Residues in contact with LEU 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P GLU* 3.7 3.6 + - - -
125P ARG* 3.4 38.8 - - - +
126P ARG* 4.2 2.2 - - - +
268T ILE* 3.1 16.3 + - + +
269T ARG* 1.3 72.1 - - - +
271T GLU* 1.3 60.6 + - - +
273T LEU* 3.1 8.5 + - + -
274T VAL* 2.9 26.0 + - - +
283T TYR* 4.1 6.7 - - + -
289T PRO 3.6 6.7 - - - +
290T GLY 4.1 0.2 - - - -
291T LEU* 3.3 44.1 - - + +
304T ILE* 3.3 49.1 - - + +
305T PHE* 4.8 2.0 - - - +
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Residues in contact with GLU 271 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P TYR* 3.7 40.6 - - + +
122P GLU* 5.0 0.2 + - - -
125P ARG* 4.0 14.6 - - - +
269T ARG* 3.5 0.8 - - - +
270T LEU* 1.3 76.1 - - - +
272T GLY* 1.3 60.6 + - - +
274T VAL* 3.2 13.4 - - - +
275T LEU* 3.0 55.3 + - + +
283T TYR* 3.4 25.4 - - - +
285T PRO* 5.1 4.0 - - - +
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Residues in contact with GLY 272 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269T ARG* 4.1 24.2 + - - +
270T LEU 3.4 0.4 - - - -
271T GLU* 1.3 77.4 - - - +
273T LEU* 1.3 51.8 + - - +
275T LEU* 3.4 9.3 + - - -
276T THR* 2.8 43.4 + - - +
335T PHE* 4.5 6.3 - - - -
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Residues in contact with LEU 273 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268T ILE* 4.8 1.3 - - + -
269T ARG 3.3 18.7 + - - +
270T LEU* 3.1 20.3 + - + +
272T GLY* 1.3 77.3 - - - +
274T VAL* 1.3 57.2 + - - +
276T THR* 3.5 4.2 + - - -
277T HIS* 2.8 62.7 + - + +
281T SER* 3.8 1.3 + - - +
291T LEU* 3.7 31.9 - - + -
293T TYR* 4.9 11.4 - - + -
304T ILE* 4.7 7.0 - - + -
328T ILE* 5.7 2.7 - - + -
331T ILE* 3.9 13.0 - - + -
332T LEU* 4.7 14.4 - - + -
335T PHE* 3.6 18.8 - - + -
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Residues in contact with VAL 274 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270T LEU 2.9 15.7 + - - +
271T GLU* 3.2 36.1 - - - +
273T LEU* 1.3 75.5 - - - +
275T LEU* 1.3 65.6 + - + +
278T GLN* 3.4 24.1 - - + +
281T SER* 3.3 22.4 - - - +
282T SER* 3.8 25.1 - - - +
283T TYR* 3.9 20.6 - - + +
291T LEU* 4.1 2.9 - - + +
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Residues in contact with LEU 275 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271T GLU* 3.0 45.6 + - + +
272T GLY* 3.8 7.6 - - - +
273T LEU 3.3 0.2 - - - -
274T VAL* 1.3 81.5 - - + +
276T THR* 1.3 60.8 + - + +
278T GLN* 3.0 17.7 + - - +
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Residues in contact with THR 276 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272T GLY* 2.8 25.2 + - - +
273T LEU 3.5 0.7 + - - -
275T LEU* 1.3 80.9 - - + +
277T HIS* 1.3 84.1 + - - +
278T GLN* 3.6 6.8 - - - +
335T PHE* 3.3 19.4 - - + -
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Residues in contact with HIS 277 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273T LEU* 2.8 31.5 + - + +
274T VAL 3.9 0.2 - - - -
276T THR* 1.3 102.3 + - - +
278T GLN* 1.3 57.2 + - - +
279T GLN 3.2 3.1 - - - -
280T PHE* 3.1 19.0 + + + +
281T SER* 2.8 32.5 + - - +
293T TYR* 4.5 23.3 - + + -
331T ILE* 3.9 29.1 - - + +
335T PHE* 3.9 17.5 - + - -
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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