Contacts of the strand formed by residues 316 - 326 (chain B) in PDB entry 4ZPK
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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B HIS* 4.1 17.7 - + - -
308B ARG* 3.8 32.3 + - + -
309B MET 3.1 26.5 - - - +
310B LEU* 4.1 5.4 - - + -
311B ALA 4.2 1.6 - - - +
315B GLY* 1.3 72.4 - - - +
317B VAL* 1.3 68.3 + - - +
318B TRP* 4.7 16.0 - + - -
346B GLU 3.8 1.0 - - - +
347B ILE* 3.0 32.7 + - - +
349B LYS* 3.4 45.9 + - + +
354B PHE* 3.4 37.7 - + - -
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Residues in contact with VAL 317 (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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264B LEU 5.0 1.6 - - - +
265B ILE* 3.6 35.2 - - + -
308B ARG* 3.2 4.5 - - - -
309B MET* 2.9 46.9 + - + +
311B ALA* 5.7 1.8 - - + +
316B TYR* 1.3 81.7 - - - +
318B TRP* 1.3 71.1 + - - +
319B LEU* 3.8 8.6 + - + +
343B VAL* 4.8 3.4 - - + -
345B SER 4.2 8.5 - - - +
346B GLU 3.7 15.0 - - - +
347B ILE* 3.5 27.1 - - + -
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Residues in contact with TRP 318 (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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266A ARG* 5.5 3.1 - - - -
285B ASP* 5.5 0.9 - - - -
306B GLN* 3.0 37.0 - - + -
307B TYR* 3.2 14.6 - - - -
308B ARG* 3.2 41.3 - - + -
316B TYR* 4.7 13.7 - + - -
317B VAL* 1.3 76.4 - - - +
319B LEU* 1.3 69.4 + - - +
343B VAL* 3.9 4.9 - - - +
344B LEU* 3.6 33.3 + - + -
345B SER* 3.1 32.8 + - - +
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Residues in contact with LEU 319 (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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244B PHE* 4.4 12.1 - - + -
265B ILE* 6.0 1.1 - - + -
305B GLY 3.2 3.1 - - - +
306B GLN* 3.3 3.8 - - - -
307B TYR* 2.8 76.5 + - + +
309B MET* 3.7 25.8 - - + -
317B VAL* 4.2 10.5 - - + +
318B TRP* 1.3 82.5 - - - +
320B GLU* 1.3 62.1 + - - +
321B THR* 4.4 5.2 - - - +
341B ASN* 4.8 7.6 - - + +
342B TYR 3.3 17.5 - - - +
343B VAL* 3.6 24.0 - - + -
344B LEU* 4.2 6.9 - - - +
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Residues in contact with GLU 320 (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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264A ILE* 6.0 4.4 - - + +
307A HIS* 3.7 28.3 + - - -
344A GLN* 4.2 7.8 - - - +
303B VAL* 3.5 22.8 - - + +
304B SER* 3.3 24.4 - - - +
305B GLY 4.0 9.2 - - - +
306B GLN* 4.4 6.4 - - - +
319B LEU* 1.3 74.8 - - - +
321B THR* 1.3 64.8 + - - +
322B GLN* 4.9 8.8 + - + -
340B VAL 3.8 1.0 - - - +
342B TYR* 2.8 50.5 + - + +
344B LEU* 4.2 12.7 - - + +
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Residues in contact with THR 321 (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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252B MET* 6.2 0.9 - - + -
302B VAL 3.9 1.0 - - - +
303B VAL* 3.7 2.4 - - - -
304B SER* 3.2 38.1 + - - -
307B TYR* 2.7 27.0 + - - -
319B LEU* 4.4 0.3 - - - +
320B GLU* 1.3 75.3 - - - +
322B GLN* 1.3 68.7 + - - +
323B GLY* 3.9 2.1 + - - +
339B CYS* 3.7 36.6 - - + -
340B VAL 3.7 3.4 - - - +
341B ASN* 2.7 22.2 + - - +
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Residues in contact with GLN 322 (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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229B ILE* 4.4 20.3 - - + +
230B GLN* 4.4 18.4 + - - +
302B VAL 3.5 6.1 - - - +
303B VAL* 4.0 26.0 - - + +
320B GLU* 4.9 9.3 + - - +
321B THR* 1.3 76.1 - - - +
323B GLY* 1.3 59.5 + - - +
324B THR* 4.9 2.1 + - - -
338B MET 3.8 0.9 - - - +
339B CYS* 3.4 2.4 - - - -
340B VAL* 2.9 56.6 + - + +
342B TYR* 3.9 29.8 + - + -
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Residues in contact with GLY 323 (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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229B ILE* 5.1 0.7 - - - +
296B LEU* 3.8 16.2 - - - -
301B GLN* 3.1 8.3 - - - +
302B VAL* 2.9 36.1 + - - +
321B THR* 3.9 4.5 + - - +
322B GLN* 1.3 71.5 - - - +
324B THR* 1.3 63.7 + - - -
338B MET 3.5 6.3 - - - -
339B CYS* 4.3 12.1 - - - -
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Residues in contact with THR 324 (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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229B ILE* 4.8 2.3 - - - +
230B GLN 4.4 2.6 + - - -
231B HIS* 3.7 25.1 - - + +
232B PRO* 4.0 19.4 - - - +
296B LEU* 4.2 0.6 - - - +
300B GLY 4.0 3.8 - - - +
301B GLN* 2.8 38.0 + - + +
322B GLN 4.9 1.9 + - - -
323B GLY* 1.3 75.9 + - - -
325B VAL* 1.3 75.1 - - - +
326B ILE* 4.0 1.9 + - + +
337B ILE* 3.5 4.0 - - - +
338B MET* 2.9 35.0 + - - +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B HIS* 5.0 0.9 + - - -
250B MET* 3.8 22.9 - - + -
296B LEU* 3.5 32.8 - - + +
300B GLY* 3.3 21.3 + - - +
324B THR* 1.3 85.2 - - - +
326B ILE* 1.3 70.8 + - - +
327B TYR* 3.4 37.0 - - + +
334B PRO* 4.7 6.7 - - + -
336B CYS 3.3 12.8 - - - +
337B ILE* 4.0 9.4 - - + -
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Residues in contact with ILE 326 (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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231B HIS* 3.6 35.0 - - + +
232B PRO* 4.9 0.9 - - + -
324B THR* 4.3 7.6 - - + +
325B VAL* 1.3 78.5 - - - +
327B TYR* 1.3 65.5 + - - +
334B PRO* 4.1 0.2 - - - +
335B GLN* 2.8 32.9 + - + +
336B CYS* 2.9 33.8 + - + +
338B MET* 3.7 37.7 - - + -
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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