Contacts of the helix formed by residues 281 - 300 (chain A) in PDB entry 4Z3A
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 ARG 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A HIS* 3.7 8.5 - - - -
279A PHE 3.9 3.5 - - - +
280A PRO* 1.3 82.3 - - + +
282A ALA* 1.4 66.5 + - - +
283A GLN* 3.6 39.6 - - + +
284A ASP* 2.9 47.1 + - - +
285A LYS* 3.6 5.9 + - - +
13C T 3.3 25.8 - - - +
14C G 3.5 26.8 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 3.6 28.9 + - + -
161A LYS* 3.8 37.2 - - + -
162A CYS* 3.4 24.6 - - - -
165A MET* 4.3 5.2 - - - -
281A ARG* 1.4 71.9 - - - +
283A GLN* 1.3 61.6 + - - +
285A LYS* 3.0 12.6 + - - +
286A VAL* 3.1 12.0 + - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 3.0 26.7 - - - +
281A ARG* 3.1 39.0 - - + +
282A ALA* 1.3 80.5 - - - +
284A ASP* 1.3 59.6 + - - +
286A VAL* 3.5 33.6 + - - +
287A HIS* 4.8 1.2 + - - +
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.4 36.4 - - + -
280A PRO* 3.3 17.5 - - - +
281A ARG* 2.9 61.7 + - - +
283A GLN* 1.3 75.4 - - - +
285A LYS* 1.3 59.3 + - - +
287A HIS* 5.1 4.9 + - - +
288A TYR* 4.9 4.5 - - - -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 2.8 31.9 + - + +
162A CYS* 4.1 9.2 - - - -
270A PRO* 4.1 21.3 - - + +
271A SER 2.8 31.4 + - - +
272A SER* 3.5 8.5 - - - -
273A SER 2.8 22.2 + - - -
274A ALA* 4.4 0.2 - - - +
276A CYS* 4.8 4.2 - - - +
279A PHE* 3.3 40.5 + - + -
281A ARG 4.0 3.4 - - - +
282A ALA 3.0 6.4 + - - +
284A ASP* 1.3 76.5 - - - +
286A VAL* 1.3 63.3 + - - +
287A HIS 3.2 3.4 - - - -
288A TYR* 3.1 20.8 + - - +
289A TYR* 3.5 18.6 - - + -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS* 4.0 8.1 - - - +
165A MET* 3.7 22.9 - - + +
166A SER* 3.7 33.7 - - - +
282A ALA 3.1 12.0 + - - +
283A GLN* 3.5 36.3 - - - +
284A ASP 3.7 0.2 - - - -
285A LYS* 1.3 75.9 - - - +
287A HIS* 1.4 65.6 + - + +
289A TYR* 3.0 18.8 + - - +
290A ILE* 3.0 24.9 + - + +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLN 4.8 1.4 + - - +
284A ASP 5.2 4.3 - - - +
285A LYS 3.2 1.2 + - - -
286A VAL* 1.4 80.5 - - - +
288A TYR* 1.4 94.1 + + + +
290A ILE* 3.4 12.9 + - - +
291A LYS* 3.0 60.0 + - + +
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PHE* 3.5 39.4 - + + +
253A GLY* 4.3 9.0 - - - -
267A TYR* 2.8 32.9 + - - +
268A VAL 4.5 1.6 - - - -
269A MET* 3.9 22.2 - - + -
270A PRO* 3.5 28.9 - - + -
279A PHE* 4.2 17.0 - + - -
284A ASP 4.9 2.9 - - - -
285A LYS* 3.1 17.6 + - - +
287A HIS* 1.4 101.1 + + + +
289A TYR* 1.4 59.3 + - + +
291A LYS* 4.5 0.7 - - + -
292A LEU* 3.0 17.2 + - - +
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 5.9 0.9 - - + -
159A PHE* 3.6 39.8 - + - -
162A CYS* 3.5 42.1 - - + +
163A LEU* 3.9 4.3 - - + -
166A SER* 3.4 21.3 - - - +
168A LEU* 3.7 19.8 - - + +
230A ASN* 4.6 2.6 + - - -
269A MET* 3.5 36.3 - - + +
270A PRO* 5.3 3.3 + - + -
272A SER* 3.8 18.9 - - - -
285A LYS* 3.5 23.3 - - + -
286A VAL* 3.0 6.0 + - - +
288A TYR* 1.4 73.1 - - - +
290A ILE* 1.3 60.2 + - - +
292A LEU* 3.2 8.7 + - + +
293A LYS* 2.9 28.6 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A MET 5.1 2.7 - - - +
166A SER* 3.9 23.8 - - - +
286A VAL* 3.0 37.4 + - + +
287A HIS* 3.6 11.4 - - - +
289A TYR* 1.3 75.9 - - - +
291A LYS* 1.3 58.9 + - + +
293A LYS* 3.3 15.8 + - - +
294A ASP* 2.9 47.9 + - - +
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.2 25.1 + - + +
287A HIS* 3.0 48.5 + - + +
288A TYR* 4.5 0.7 - - + -
290A ILE* 1.3 75.5 - - + +
292A LEU* 1.3 54.5 + - - +
294A ASP* 3.7 16.5 - - - +
295A LEU* 2.8 34.5 + - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 4.0 28.3 - - + -
136A ILE* 4.7 4.7 - - + -
168A LEU* 4.3 14.4 - - + -
226A ILE* 4.0 18.2 - - + -
228A VAL* 3.7 42.4 - - + -
267A TYR* 3.6 19.4 + - + -
269A MET* 4.3 12.8 - - + -
288A TYR 3.0 18.6 + - - +
289A TYR* 3.4 6.1 - - + +
290A ILE 3.2 0.2 - - - -
291A LYS* 1.3 72.9 - - - +
293A LYS* 1.4 54.5 + - - +
295A LEU* 3.2 4.8 + - + +
296A ARG* 2.8 32.6 + - - +
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER 2.8 27.9 + - - +
167A GLY* 4.1 19.0 - - - +
168A LEU* 3.8 18.3 - - + +
289A TYR 2.9 13.4 + - - +
290A ILE* 3.4 16.8 - - - +
292A LEU* 1.4 76.3 - - - +
294A ASP* 1.4 70.2 + - - +
296A ARG* 3.3 24.9 + - - +
297A ASP* 2.9 44.8 + - - +
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Residues in contact with ASP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ILE* 2.9 33.9 + - - +
291A LYS* 3.7 20.6 - - + +
292A LEU 3.3 0.2 - - - -
293A LYS* 1.4 83.8 - - - +
295A LEU* 1.4 66.3 + - - +
297A ASP* 3.4 8.2 + - - +
298A GLN* 3.1 24.9 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ILE* 4.0 25.1 - - + -
254A LEU* 3.8 35.4 - - + -
265A LEU* 4.2 18.4 - - + -
267A TYR* 3.9 21.8 - - + -
291A LYS 2.8 21.8 + - - +
292A LEU* 3.5 5.6 - - + +
294A ASP* 1.4 72.7 - - - +
296A ARG* 1.4 62.4 + - - +
298A GLN* 3.4 23.8 + - - +
299A LEU* 3.1 26.8 + - + +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.8 36.1 - - + -
134A ILE* 4.3 14.3 - - + +
167A GLY 5.4 2.8 + - - -
168A LEU* 3.6 31.4 + - - +
185A TYR* 4.3 14.7 + - - +
187A ILE* 5.4 2.0 - - - +
225A ARG* 5.8 2.0 - - - -
226A ILE* 3.9 16.1 - - + +
292A LEU 2.8 20.1 + - - +
293A LYS* 3.3 23.0 + - - +
295A LEU* 1.4 70.5 - - - +
297A ASP* 1.4 87.8 + - - +
299A LEU* 3.3 4.9 + - - +
300A LYS* 3.1 36.6 + - + +
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Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LYS* 2.9 32.3 + - - +
294A ASP* 3.9 8.6 - - - +
296A ARG* 1.4 103.9 + - - +
298A GLN* 1.3 60.6 + - - +
300A LYS* 3.4 9.2 + - - +
301A GLY* 3.4 18.2 + - - -
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ASP 3.1 17.6 + - - +
295A LEU* 3.5 25.6 - - - +
297A ASP* 1.3 73.4 - - - +
299A LEU* 1.4 70.1 + - - +
301A GLY* 3.4 18.4 + - - -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.7 35.8 + - + +
226A ILE* 3.6 38.1 - - + -
265A LEU* 3.8 26.9 - - + -
295A LEU* 3.1 21.9 + - + +
296A ARG* 3.3 4.9 + - - +
298A GLN* 1.4 81.3 - - - +
300A LYS* 1.4 58.1 + - - +
301A GLY 3.2 7.7 + - - +
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.1 42.6 + - - +
225A ARG* 4.1 26.8 - - - +
296A ARG* 3.1 32.4 + - + +
297A ASP* 3.4 8.7 + - - +
298A GLN 3.3 0.2 - - - -
299A LEU* 1.4 74.3 - - - +
301A GLY* 1.3 55.1 + - - +
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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
------------------------------------------------------------
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