Contacts of the strand formed by residues 288 - 295 (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 PHE 288 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU* 5.0 4.3 - - + -
62A CYS* 6.2 1.3 - - - -
65A HIS* 3.5 37.0 - + + -
69A LEU* 4.3 15.9 - - + -
72A LEU* 4.8 8.3 - - + -
283T TYR* 3.9 3.5 - - - -
284T GLU 2.9 22.4 + - - +
285T PRO 4.1 0.9 - - - -
286T GLU 3.7 0.2 - - - -
287T LEU* 1.3 85.2 - - + +
289T PRO* 1.4 70.2 - - + +
290T GLY* 3.1 49.3 + - - +
292T ILE* 3.6 18.8 - - + +
303T LEU* 3.6 36.6 - - + -
305T PHE* 4.1 16.6 - + - -
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Residues in contact with PRO 289 (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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61A GLU* 3.9 22.7 - - + +
65A HIS* 3.5 28.0 - - + +
125P ARG* 3.4 2.3 + - - -
126P ARG* 2.7 45.9 + - - +
270T LEU* 3.6 0.7 - - - +
283T TYR* 3.2 21.7 - - + +
285T PRO 4.1 14.3 - - - +
288T PHE* 1.4 88.7 - - + +
290T GLY* 1.3 54.4 + - - +
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Residues in contact with GLY 290 (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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126P ARG* 3.4 5.7 - - - +
270T LEU* 4.1 0.4 - - - -
283T TYR* 3.7 4.9 - - - -
288T PHE* 3.1 39.9 + - - +
289T PRO* 1.3 82.8 - - - +
291T LEU* 1.3 62.7 + - - -
292T ILE* 3.8 3.1 + - - +
304T ILE 3.2 13.9 - - - -
305T PHE* 3.7 9.8 - - - -
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Residues in contact with LEU 291 (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* 3.3 52.0 - - + +
273T LEU* 3.7 28.9 - - + -
274T VAL* 4.1 16.2 - - + -
281T SER* 3.7 13.0 - - - -
282T SER 4.2 5.8 - - - +
283T TYR* 4.1 10.3 - - + -
290T GLY* 1.3 72.6 - - - -
292T ILE* 1.3 80.8 + - - +
293T TYR* 3.8 5.6 - - + -
302T LEU 2.9 13.5 - - - +
303T LEU* 3.1 2.7 - - - -
304T ILE* 3.0 36.9 + - + +
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Residues in contact with ILE 292 (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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72A LEU* 3.9 28.7 - - + -
74A LEU* 6.1 0.2 - - + -
281T SER* 3.4 22.5 - - - -
282T SER* 3.5 27.5 + - - +
283T TYR* 5.6 1.6 - - - -
288T PHE* 3.6 26.2 - - + +
290T GLY 3.9 2.5 - - - +
291T LEU* 1.3 75.6 - - - +
293T TYR* 1.3 62.0 + - - +
294T ARG* 4.1 29.2 + - + +
301T VAL* 3.8 24.7 - - + -
302T LEU 3.2 4.0 - - - -
303T LEU* 3.7 17.9 - - + -
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Residues in contact with TYR 293 (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* 4.9 10.1 - - + -
277T HIS* 4.5 21.9 - + + -
280T PHE* 3.7 38.8 - + + -
281T SER* 4.3 9.9 - - - -
291T LEU* 3.8 13.4 + - + -
292T ILE* 1.3 72.5 - - - +
294T ARG* 1.3 58.8 + - - +
295T MET* 3.4 41.9 + - + +
300T ILE 3.2 7.6 - - - +
301T VAL* 3.4 0.7 - - - -
302T LEU* 2.9 40.6 + - + +
304T ILE* 3.9 13.7 - - + -
328T ILE* 3.6 24.5 - - + -
331T ILE* 5.8 6.0 - - + +
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Residues in contact with ARG 294 (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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72A LEU* 3.1 39.8 + - - +
73A GLY* 3.6 22.0 + - - -
74A LEU* 5.8 0.6 - - - +
280T PHE* 2.9 40.0 + - - +
281T SER* 5.9 0.2 - - - -
282T SER* 5.4 5.9 + - - -
292T ILE* 4.2 19.5 - - + +
293T TYR* 1.3 73.4 - - - +
295T MET* 1.3 64.0 + - - +
296T ILE* 3.7 8.7 + - + +
300T ILE 3.7 4.0 - - - -
301T VAL* 4.1 25.2 - - + +
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Residues in contact with MET 295 (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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280T PHE* 5.1 1.6 - - - -
293T TYR* 3.4 35.6 + - + +
294T ARG* 1.3 73.6 - - - +
296T ILE* 1.3 63.1 + - - +
297T LYS 3.7 21.5 - - - +
298T PRO* 2.9 24.2 - - - +
299T ARG* 3.0 5.4 - - - -
300T ILE 2.8 26.3 + - - +
302T LEU* 4.3 6.1 - - + -
324T ALA* 3.4 43.5 - - - +
327T ASN* 3.7 17.3 - - + -
328T ILE* 4.0 11.2 - - + -
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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