Contacts of the strand formed by residues 304 - 309 (chain B) 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 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B GLU 3.9 4.0 + - - +
265B VAL* 3.9 14.3 - - + -
266B THR* 2.9 29.8 + - - +
267B HIS* 4.7 0.7 - + - -
284B LEU* 4.4 13.9 - - + -
288B PHE* 3.8 24.5 - + + -
299B TYR* 3.3 17.7 - + + +
303B CYS* 1.3 75.1 - - - +
305B LYS* 1.3 75.1 + - - +
306B THR* 3.1 25.1 - - + -
321B SER 3.3 4.0 - - - -
323B SER* 3.5 19.7 - - - -
346B LEU* 5.8 3.8 - - + -
349B SER* 4.3 4.0 - - - -
350B LEU* 3.5 20.0 - - + -
353B GLN* 3.3 36.6 - - - -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B VAL* 3.7 22.7 - - + -
216B SER 2.4 32.3 + - - +
217B ASN 3.2 9.1 + - - -
218B GLY 2.9 28.7 + - - +
236B TYR* 5.3 6.4 - - + +
266B THR* 3.3 17.0 - - + +
268B PHE* 4.8 4.3 - - + -
302B SER* 6.1 0.2 - - - -
303B CYS* 4.8 9.0 - - + -
304B PHE* 1.3 81.9 - - - +
306B THR* 1.3 65.3 + - - +
321B SER* 2.6 32.3 + - - +
322B MET* 2.8 32.4 - - + -
323B SER 2.9 5.2 + - - -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B THR 3.0 6.3 + - - -
267B HIS* 3.3 25.7 + - + +
268B PHE* 2.9 29.0 + - - +
269B CYS* 5.5 0.3 - - - -
304B PHE* 3.1 33.4 - - + -
305B LYS* 1.3 72.1 - - - +
307B VAL* 1.3 66.0 + - - +
308B PHE* 3.6 27.2 - - + -
323B SER* 3.2 19.3 - - - +
325B PHE* 3.6 7.6 - - + -
346B LEU* 5.2 3.4 - - + -
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 4.5 15.9 - - + -
250B ALA* 3.6 32.8 - - + -
253B PRO* 4.9 5.8 - - + -
268B PHE* 3.5 26.2 - - + +
306B THR* 1.3 78.5 - - - +
308B PHE* 1.3 73.9 + - - +
309B ILE* 3.8 17.9 - - + -
322B MET* 5.0 1.1 - - + -
323B SER 3.0 6.3 + - - +
324B ILE* 3.5 20.5 - - + -
325B PHE* 2.9 27.0 + - - +
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 5.5 1.4 - - - +
267B HIS* 5.4 2.7 - + - -
268B PHE 3.0 11.8 + - - +
269B CYS* 3.5 27.5 - - + -
270B LEU* 4.5 13.7 + - - +
273B LEU* 6.3 0.2 - - + -
277B LEU* 3.6 15.9 - - + -
280B THR* 4.5 12.8 - - + -
281B THR* 5.6 0.4 - - - -
306B THR* 3.6 14.6 - - + -
307B VAL* 1.3 84.6 - - - +
309B ILE* 1.3 68.0 + - - +
325B PHE* 3.1 42.6 - + - +
326B SER 4.1 8.7 - - - +
327B THR* 3.2 14.5 + - + +
329B LEU 4.5 6.3 - - - -
330B LEU* 3.5 36.8 - - + -
346B LEU* 5.7 4.9 - - + -
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B HIS* 3.3 29.6 - - + +
178B PHE* 3.5 45.1 - - + -
250B ALA* 4.4 1.6 - - + -
270B LEU* 5.0 1.6 - - - -
307B VAL* 3.8 11.7 - - + -
308B PHE* 1.3 79.6 - - - +
310B ASP* 1.3 60.1 + - - +
311B GLU 3.0 29.3 + - - +
324B ILE* 3.6 26.0 - - + -
325B PHE* 2.9 9.4 + - - +
326B SER* 3.2 6.9 - - - -
327B THR* 2.7 31.1 + - - -
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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