Contacts of the helix formed by residues 287 - 300 (chain B) in PDB entry 1Z6T
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 GLY 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B GLU* 5.3 2.8 + - - -
285B SER* 3.8 1.8 + - - -
286B LEU* 1.3 83.6 - - - +
288B LYS* 1.3 66.1 + - - -
289B GLU* 3.4 3.1 + - - -
290B LYS* 3.5 6.5 + - - +
291B GLY* 3.0 21.1 + - - -
314B ILE* 5.0 1.8 - - - +
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Residues in contact with LYS 288 (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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286B LEU 3.9 0.4 + - - -
287B GLY* 1.3 69.8 - - - -
289B GLU* 1.3 61.5 + - + +
291B GLY* 3.2 2.6 + - - -
292B LEU* 2.8 50.2 + - + +
311B HIS* 2.4 46.7 + - + +
314B ILE* 3.5 24.2 - - + +
315B LYS* 3.5 20.4 - - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLY* 3.4 1.0 - - - -
288B LYS* 1.3 81.6 - - + +
290B LYS* 1.3 59.9 + - + +
292B LEU* 3.4 21.0 + - - +
293B GLU* 2.8 28.3 + - - +
303B LYS* 2.7 40.4 + - - +
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Residues in contact with LYS 290 (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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127B VAL* 3.8 12.1 - - + +
128B THR* 2.7 48.9 + - - +
129B ARG* 5.1 3.1 - - + +
130B LYS 6.0 0.4 - - - +
286B LEU* 3.6 29.4 - - + -
287B GLY* 3.5 7.6 + - - +
288B LYS 3.4 0.2 - - - -
289B GLU* 1.3 79.6 - - + +
291B GLY* 1.3 59.6 + - - +
293B GLU* 2.7 30.4 + - - +
294B ILE* 3.0 32.2 + - - +
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Residues in contact with GLY 291 (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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286B LEU* 3.8 13.3 - - - +
287B GLY 3.0 14.7 + - - -
288B LYS 3.6 3.4 - - - -
290B LYS* 1.3 74.1 - - - +
292B LEU* 1.3 63.4 + - - +
294B ILE* 3.3 2.2 + - - -
295B LEU 3.1 17.2 + - - -
314B ILE* 3.5 20.1 - - - +
324B VAL* 3.4 20.3 - - - +
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Residues in contact with LEU 292 (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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288B LYS* 2.8 33.1 + - + +
289B GLU* 3.6 25.6 - - - +
291B GLY* 1.3 71.5 - - - +
293B GLU* 1.3 56.7 + - - +
295B LEU* 3.3 5.9 + - + +
296B SER* 2.9 28.9 + - - -
303B LYS* 3.9 14.4 - - + +
306B LEU* 3.7 8.8 - - + +
310B ALA* 3.9 24.0 - - + +
311B HIS* 3.6 40.4 - - + +
314B ILE* 3.7 22.1 - - + +
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Residues in contact with GLU 293 (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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127B VAL* 3.7 18.9 - - + +
128B THR* 5.1 1.2 + - - -
289B GLU 2.8 17.6 + - - +
290B LYS* 2.7 45.3 + - - +
291B GLY 3.3 0.4 - - - -
292B LEU* 1.3 72.7 - - - +
294B ILE* 1.3 64.0 + - - +
296B SER* 2.9 24.5 + - - +
297B LEU* 3.1 27.8 + - + +
303B LYS* 3.8 20.2 + - + +
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Residues in contact with ILE 294 (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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125B VAL* 3.9 7.8 - - + +
127B VAL* 3.7 21.5 - - + +
286B LEU* 3.5 30.5 - - + -
290B LYS 3.0 14.4 + - - +
291B GLY 3.5 7.0 - - - +
292B LEU 3.3 0.2 - - - -
293B GLU* 1.3 74.2 - - - +
295B LEU* 1.3 62.9 + - - +
297B LEU* 3.2 4.7 + - - +
298B PHE* 3.1 45.7 + - + -
321B PRO* 4.5 9.0 - - + +
324B VAL* 3.7 22.9 - - + +
325B SER* 4.1 9.2 - - - +
901B ADP 3.9 24.5 - - + +
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Residues in contact with LEU 295 (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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291B GLY 3.1 13.8 + - - +
292B LEU* 3.4 9.6 - - - +
294B ILE* 1.3 78.7 - - - +
296B SER* 1.3 57.3 + - - +
298B PHE* 3.3 4.9 + - - +
299B VAL* 3.0 35.8 + - - +
306B LEU* 4.7 3.4 - - + -
310B ALA* 4.1 20.2 - - + +
313B ILE* 4.4 8.1 - - + -
314B ILE* 3.7 21.5 - - + -
324B VAL* 3.8 16.2 - - + +
327B ILE* 4.6 4.3 - - + -
328B GLY* 3.7 28.0 - - - +
331B LEU* 4.4 9.9 - - + -
338B TRP* 4.1 26.2 - - + -
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Residues in contact with SER 296 (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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292B LEU 2.9 15.9 + - - -
293B GLU* 2.9 27.7 + - - +
295B LEU* 1.3 73.2 - - - +
297B LEU* 1.3 61.1 + - - +
299B VAL* 4.1 7.4 - - - -
300B ASN* 2.9 22.3 + - - -
301B MET 3.0 32.1 + - - +
302B LYS 4.2 0.7 - - - -
303B LYS* 3.8 23.4 + - - +
306B LEU* 4.2 7.6 - - - +
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Residues in contact with LEU 297 (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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125B VAL* 3.6 22.0 - - + +
126B PHE 3.6 25.1 - - - +
127B VAL* 3.7 20.2 - - + -
293B GLU* 3.1 25.1 + - + +
294B ILE 3.2 4.9 + - - +
296B SER* 1.3 79.8 - - - +
298B PHE* 1.3 65.9 + - - +
300B ASN* 3.6 10.1 + - - +
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Residues in contact with PHE 298 (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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124B VAL* 4.0 17.5 - - + -
125B VAL* 3.6 33.7 - - + -
294B ILE* 3.1 38.1 + - + -
295B LEU 3.3 7.8 + - - +
297B LEU* 1.3 79.3 - - - +
299B VAL* 1.3 59.0 + - - +
300B ASN* 3.3 2.1 + - - +
325B SER* 3.6 30.5 - - - -
328B GLY* 3.3 28.7 - - - +
329B ALA* 3.6 21.1 - - + -
332B ARG* 3.2 52.6 - - - +
420B ASN 4.7 0.7 - - - -
422B SER* 4.5 1.6 - - - -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.0 21.3 + - - +
296B SER 4.0 1.8 - - - +
298B PHE* 1.3 76.2 - - + +
300B ASN* 1.3 69.0 + - - +
301B MET* 3.3 43.1 - - + +
306B LEU* 4.0 11.2 - - + -
328B GLY 4.3 2.9 - - - +
331B LEU* 3.7 35.7 - - + +
332B ARG* 4.0 11.9 - - - +
335B PRO* 6.5 0.2 - - + -
338B TRP* 4.2 11.0 - - + +
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Residues in contact with ASN 300 (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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296B SER 2.9 8.4 + - - -
297B LEU* 3.6 7.8 + - - +
298B PHE 3.3 5.2 - - - +
299B VAL* 1.3 82.0 - - - +
301B MET* 1.3 60.9 + - - +
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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