Contacts of the helix formed by residues 287 - 300 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C GLU* 5.8 0.6 + - - -
285C SER* 3.8 1.8 + - - -
286C LEU* 1.3 82.3 - - - +
288C LYS* 1.3 66.4 + - - -
289C GLU 3.3 2.7 - - - -
290C LYS* 3.4 7.7 + - - +
291C GLY* 3.0 20.6 + - - -
314C ILE* 5.0 1.4 - - - +
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C LEU 3.9 0.4 + - - -
287C GLY* 1.3 70.3 - - - -
289C GLU* 1.3 59.4 + - + +
291C GLY* 3.3 2.3 + - - -
292C LEU* 2.8 49.8 + - + +
311C HIS* 2.4 44.9 + - - +
314C ILE* 3.4 25.2 - - + +
315C LYS* 3.5 21.2 - - - +
47D PRO 6.1 0.7 - - - -
48D THR* 4.2 13.0 - - + -
407D GLU* 3.4 38.6 + - - +
409D GLU* 5.1 6.1 - - - +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C GLY 3.3 0.8 - - - -
288C LYS* 1.3 78.6 - - + +
290C LYS* 1.3 59.6 + - + +
292C LEU* 3.4 6.6 + - - +
293C GLU* 2.9 28.6 + - - +
303C LYS* 2.7 42.5 + - - +
48D THR* 2.4 37.8 + - - +
50D GLN* 3.5 49.9 - - + +
51D GLN* 3.2 18.9 + - - +
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 3.8 12.4 - - + +
128C THR* 2.7 51.9 + - - +
129C ARG* 5.1 3.8 - - + +
130C LYS 6.0 0.2 - - - +
286C LEU* 3.7 28.3 - - + -
287C GLY* 3.4 9.4 + - - +
288C LYS 3.3 0.2 - - - -
289C GLU* 1.3 77.9 - - + +
291C GLY* 1.3 58.3 + - - +
293C GLU* 2.9 31.2 + - - +
294C ILE* 3.1 31.5 + - - +
50D GLN* 6.2 1.8 - - - +
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Residues in contact with GLY 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 4.0 13.5 - - - +
287C GLY 3.0 14.5 + - - -
288C LYS 3.6 2.9 - - - -
290C LYS* 1.3 74.9 - - - +
292C LEU* 1.3 62.0 + - - +
294C ILE* 3.3 5.6 + - - +
295C LEU* 3.1 17.7 + - - +
314C ILE* 3.6 20.1 - - - +
324C VAL* 3.4 17.0 - - - +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LYS* 2.8 33.2 + - + +
289C GLU* 3.5 15.7 - - - +
291C GLY* 1.3 72.1 - - - +
293C GLU* 1.3 58.2 + - - +
295C LEU* 3.4 6.0 + - + +
296C SER* 2.9 28.4 + - - -
303C LYS* 3.9 12.8 - - + +
306C LEU* 3.6 9.8 - - + +
310C ALA* 3.9 24.7 - - + +
311C HIS* 3.6 39.3 - - + +
314C ILE* 3.8 20.1 - - + +
48D THR* 3.8 17.0 - - + -
51D GLN* 4.4 4.9 - - - +
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 3.6 18.7 - - + +
128C THR* 5.0 1.0 + - - -
289C GLU 2.9 16.9 + - - +
290C LYS* 2.9 43.5 + - - +
291C GLY 3.2 0.4 - - - -
292C LEU* 1.3 72.5 - - - +
294C ILE* 1.3 64.7 + - - +
296C SER* 2.9 23.3 + - - +
297C LEU* 3.1 27.5 + - + +
303C LYS* 3.9 21.0 + - - +
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 3.9 8.0 - - + +
127C VAL* 3.7 21.3 - - + -
286C LEU* 3.5 30.1 - - + -
290C LYS 3.1 15.1 + - - +
291C GLY* 3.3 7.4 + - - +
293C GLU* 1.3 72.4 - - - +
295C LEU* 1.3 66.6 + - - +
297C LEU* 3.2 4.7 + - - +
298C PHE* 3.0 46.7 + - + -
321C PRO* 4.5 9.2 - - + +
324C VAL* 3.8 23.1 - - + +
325C SER* 4.1 7.9 - - - +
902C ADP 3.9 24.7 - - + +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLY 3.1 12.1 + - - +
292C LEU* 3.4 9.9 - - - +
294C ILE* 1.3 79.0 - - - +
296C SER* 1.3 55.9 + - - +
298C PHE* 3.2 6.7 + - - +
299C VAL* 3.0 34.6 + - - +
306C LEU* 4.7 2.9 - - + -
310C ALA* 3.9 25.6 - - + +
313C ILE* 4.5 6.5 - - + -
314C ILE* 3.6 28.5 - - + -
324C VAL* 4.0 11.4 - - + +
327C ILE* 4.6 5.8 - - + -
328C GLY* 3.7 30.3 - - - +
331C LEU* 4.2 13.0 - - + -
338C TRP* 4.2 15.7 - - + -
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU 2.9 14.1 + - - -
293C GLU* 2.9 22.9 + - - +
295C LEU* 1.3 76.0 - - - +
297C LEU* 1.3 61.0 + - - +
299C VAL* 3.9 8.3 - - - -
300C ASN* 2.9 23.7 + - - -
301C MET 3.0 31.3 + - - +
302C LYS 4.3 0.2 - - - -
303C LYS* 4.0 22.1 + - - +
306C LEU* 4.2 7.1 - - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 3.5 27.6 - - + +
126C PHE 3.6 25.1 - - - +
127C VAL* 3.7 20.4 - - + -
293C GLU* 3.1 21.6 + - + +
294C ILE 3.2 0.6 + - - +
296C SER* 1.3 81.2 + - - +
298C PHE* 1.3 65.8 + - - +
300C ASN* 3.7 9.4 + - - +
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Residues in contact with PHE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 3.9 17.3 - - + -
125C VAL* 3.7 33.4 - - + -
294C ILE* 3.0 31.3 + - + -
295C LEU 3.5 7.2 - - - +
297C LEU* 1.3 78.8 - - - +
299C VAL* 1.3 58.9 + - - +
300C ASN* 3.3 2.1 + - - +
325C SER* 3.6 38.1 - - - -
328C GLY* 3.3 27.8 - - - +
329C ALA* 3.7 17.3 - - + -
332C ARG* 3.1 57.6 - - - +
420C ASN 4.6 0.7 - - - -
422C SER* 4.3 2.2 - - - -
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 3.0 22.8 + - - +
296C SER* 3.9 7.2 - - - +
298C PHE* 1.3 75.7 - - - +
300C ASN* 1.3 69.3 + - - +
301C MET* 3.2 41.9 - - + +
306C LEU* 4.0 8.3 - - + -
328C GLY 4.3 2.5 - - - +
331C LEU* 3.7 33.7 - - + +
332C ARG* 4.1 12.3 - - - +
338C TRP* 4.0 12.3 - - + +
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Residues in contact with ASN 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C SER 2.9 10.6 + - - -
297C LEU* 3.7 7.3 + - - +
298C PHE 3.3 4.9 - - - +
299C VAL* 1.3 81.1 - - - +
301C MET* 1.3 58.3 + - - +
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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