Contacts of the helix formed by residues 247 - 265 (chain B) in PDB entry 4ZTZ
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 THR 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 5.8 1.8 - - + -
243B THR* 3.7 9.6 - - - +
244B PRO* 3.1 25.7 + - + +
246B ARG* 1.3 101.8 - - - +
248B SER* 1.3 60.4 + - - +
249B ASN 3.6 1.6 - - - -
250B GLN* 3.6 29.6 + - - +
251B TRP* 3.0 39.0 + - + +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 3.9 10.1 + - - +
244B PRO 3.1 14.1 + - - -
245B PRO* 3.2 20.8 + - - +
246B ARG 3.7 0.4 - - - -
247B THR* 1.3 74.5 - - - +
249B ASN* 1.3 65.7 + - - +
251B TRP* 3.2 5.4 + - - +
252B LEU* 2.9 27.0 + - - +
305B ASN* 3.7 26.9 - - - -
334B CYS* 3.3 17.3 - - - +
336B LEU* 4.8 3.8 - - - +
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO 5.4 2.1 - - - +
248B SER* 1.3 77.7 - - - +
250B GLN* 1.3 59.8 + - + +
252B LEU* 3.1 10.8 + - + +
253B ASP* 2.9 30.3 + - - +
285B LYS* 4.6 21.2 - - - +
305B ASN* 4.2 15.4 - - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205A GLY 5.1 6.1 + - - -
1206A MET* 6.1 6.3 - - - +
1207A GLU* 3.8 20.8 + - - -
246B ARG* 5.0 10.5 + - - +
247B THR* 3.6 29.5 + - - +
248B SER 3.2 0.4 - - - -
249B ASN* 1.3 79.9 - - + +
251B TRP* 1.3 57.2 + - + +
253B ASP* 3.9 4.6 - - - +
254B PHE* 2.9 28.2 + - - +
257B ARG* 5.6 0.2 + - - -
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Residues in contact with TRP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLN* 5.7 1.6 - - - -
205B PRO* 3.8 19.5 - - + +
241B TRP* 3.3 54.3 - + + +
243B THR* 3.0 19.8 + - + +
247B THR* 3.0 42.3 + - - +
248B SER 3.2 5.2 + - - +
250B GLN* 1.3 77.3 - - - +
252B LEU* 1.3 60.0 + - - +
254B PHE* 3.3 49.3 - + + +
255B TRP* 2.9 39.9 + - - -
336B LEU* 3.8 4.5 - - + -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER 2.9 13.6 + - - +
249B ASN* 3.3 16.8 - - - +
251B TRP* 1.3 77.7 - - - +
253B ASP* 1.3 57.4 + - - +
255B TRP* 3.5 1.0 + - - +
256B LEU* 2.9 29.3 + - - +
285B LYS* 4.0 37.2 - - + +
287B ASN* 3.6 25.4 - - - +
303B LEU* 4.1 27.4 - - + +
304B TRP 4.8 0.9 - - - +
305B ASN* 4.3 9.4 - - + -
336B LEU* 3.7 26.6 - - + +
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Residues in contact with ASP 253 (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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1202A ASN* 4.7 15.3 + - - -
249B ASN 2.9 15.4 + - - +
250B GLN* 3.9 5.5 - - - +
252B LEU* 1.3 73.8 - - - +
254B PHE* 1.3 65.9 + - - +
256B LEU* 3.3 19.4 + - - +
257B ARG* 2.9 57.7 + - - +
287B ASN* 5.6 0.4 - - - +
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Residues in contact with PHE 254 (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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122B ARG* 4.2 12.8 - - - -
250B GLN 2.9 19.5 + - - +
251B TRP* 3.3 44.6 - + + +
253B ASP* 1.3 77.9 + - - +
255B TRP* 1.3 87.2 + + - +
257B ARG* 3.3 20.2 + - - +
258B HIS* 2.9 72.8 + + - -
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Residues in contact with TRP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 4.6 15.0 - - + -
122B ARG* 3.6 43.5 - - - -
125B VAL* 5.3 0.7 - - + -
239B LEU* 3.7 25.4 - - + -
241B TRP* 3.4 53.9 - + + -
251B TRP* 2.9 34.2 + + - +
252B LEU 4.0 0.7 - - - +
254B PHE* 1.3 88.0 - + - +
256B LEU* 1.3 61.2 + - - +
258B HIS* 4.4 5.6 - - + -
259B ARG* 2.9 50.5 + - + +
303B LEU* 3.7 17.5 - - + -
336B LEU* 3.4 20.9 - - + -
338B VAL* 5.3 6.5 - - + -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU 2.9 19.0 + - - +
253B ASP* 3.3 20.6 - - - +
255B TRP* 1.3 76.5 - - - +
257B ARG* 1.3 67.7 + - + +
259B ARG* 4.1 1.1 - - - +
260B LEU* 3.0 31.0 + - + +
275B SER* 3.8 27.6 - - - +
277B ASP* 4.5 9.2 - - - +
287B ASN* 3.4 44.9 - - + +
289B LEU* 4.1 12.7 - - + +
303B LEU* 3.7 8.9 - - + +
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLU* 3.4 35.9 + - - -
1199A THR 6.0 2.2 - - - -
1201A SER* 6.0 2.2 - - - -
250B GLN 5.6 0.2 + - - -
253B ASP* 2.9 40.9 + - - +
254B PHE* 3.8 31.5 - - - +
256B LEU* 1.3 82.0 - - + +
258B HIS* 1.3 70.6 + - - +
260B LEU* 3.7 6.5 + - - +
261B GLN* 2.9 30.0 + - - +
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Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLU* 5.5 1.4 + - - -
122B ARG* 3.0 31.2 + - - +
254B PHE* 2.9 66.5 + + - +
255B TRP* 4.1 13.0 - - + +
257B ARG* 1.3 93.5 + - - +
259B ARG* 1.3 61.9 + - - +
261B GLN* 3.3 12.1 + - - +
262B TRP* 2.9 27.2 + - - +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 3.1 28.7 - - - -
117B SER 4.9 1.0 + - - -
118B VAL* 3.7 21.6 - - - +
239B LEU* 6.3 0.4 - - - -
255B TRP* 2.9 42.1 + - + +
256B LEU 4.1 1.1 - - - +
258B HIS* 1.3 72.1 - - - +
260B LEU* 1.3 66.8 + - - +
262B TRP* 2.9 42.7 + - - +
263B TRP* 2.9 40.6 + - - +
289B LEU* 4.3 5.2 - - + -
301B GLU* 3.0 49.5 + - - +
303B LEU* 4.4 6.5 - - + -
338B VAL* 3.6 22.4 - - + -
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Residues in contact with LEU 260 (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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256B LEU* 3.0 23.0 + - + +
257B ARG* 3.9 5.6 - - - +
259B ARG* 1.3 76.3 - - - +
261B GLN* 1.3 57.0 + - - +
263B TRP* 3.4 1.8 + - + -
264B ARG* 2.9 76.0 + - + +
273B PHE* 4.1 16.6 - - + +
274B SER 4.2 14.4 - - - +
275B SER* 3.7 26.2 - - - +
289B LEU* 3.9 20.9 - - + +
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Residues in contact with GLN 261 (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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454A GLU* 2.9 42.6 + - + +
457A ARG* 5.3 1.8 - - - +
117B SER* 5.4 2.1 + - - -
257B ARG 2.9 20.3 + - - +
258B HIS* 3.5 12.6 + - - +
259B ARG 3.1 0.2 - - - -
260B LEU* 1.3 76.8 - - - +
262B TRP* 1.3 70.2 + - - +
264B ARG* 3.3 6.8 + - - +
265B LYS* 3.3 43.4 + - - +
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Residues in contact with TRP 262 (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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110B LEU* 3.5 36.6 - - + -
113B GLU* 3.2 22.3 + - + +
114B TRP* 3.5 33.8 - + + +
117B SER* 3.6 26.8 - - - +
258B HIS 2.9 12.3 + - - +
259B ARG* 2.9 41.3 + - - +
261B GLN* 1.3 84.5 + - - +
263B TRP* 1.3 95.8 + + - +
265B LYS* 3.2 32.2 - - - +
266B PHE* 3.5 18.9 - + - -
342B LEU* 4.7 3.8 - - + -
349B TYR* 4.6 1.6 - - - -
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Residues in contact with TRP 263 (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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110B LEU* 5.5 1.6 - - + -
114B TRP* 4.3 1.6 - + - -
259B ARG* 2.9 32.6 + - - +
260B LEU* 4.0 6.1 - - - +
261B GLN 3.2 0.2 - - - -
262B TRP* 1.3 93.1 - + - +
264B ARG* 1.3 61.0 + - - +
265B LYS 3.0 13.3 - - - +
273B PHE* 3.2 54.8 - + + -
289B LEU* 4.5 7.4 - - + -
300B ILE* 4.0 28.1 - - + +
301B GLU* 3.2 37.5 - - + -
340B GLY* 4.3 5.8 - - - -
341B ASP 4.1 13.9 - - - -
342B LEU* 4.0 23.8 - - + -
345B GLY* 4.2 18.7 + - - -
349B TYR* 3.0 36.5 + + - -
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ARG* 3.7 13.2 + - - +
260B LEU* 2.9 49.0 + - + +
261B GLN* 3.3 6.7 + - - +
263B TRP* 1.3 73.2 - - - +
265B LYS* 1.3 62.0 + - - +
267B ALA* 3.9 5.1 + - - +
270B PRO* 3.3 50.5 + - + +
271B SER* 5.6 2.0 + - - +
273B PHE* 3.0 39.0 + - + -
274B SER* 4.2 6.1 - - - +
275B SER* 4.9 1.6 + - - +
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Residues in contact with LYS 265 (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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457A ARG* 3.7 27.6 - - - +
113B GLU* 6.0 0.4 - - - +
117B SER* 4.4 10.5 + - - -
261B GLN* 3.3 28.4 + - - +
262B TRP* 3.2 39.1 - - - +
263B TRP 3.0 15.4 - - - +
264B ARG* 1.3 74.8 - - - +
266B PHE* 1.3 99.8 + - + +
267B ALA 2.9 11.9 + - - +
349B TYR* 3.4 4.0 + - - -
375B HIS* 5.9 0.7 - - + +
483B LYS* 5.5 12.7 + - - +
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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
------------------------------------------------------------
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