Contacts of the helix formed by residues 274 - 288 (chain A) in PDB entry 4R1Z
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 ASP 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ALA* 5.0 2.0 - - - -
148A PHE* 4.2 7.6 - - - -
194A ALA 4.1 2.0 - - - +
195A LEU 3.7 7.0 - - - +
196A CYS 3.2 21.8 - - - +
197A PHE 2.8 26.7 - - - +
198A ASN* 3.0 11.3 + - - +
263A HIS* 2.8 19.0 - - - -
272A GLN* 3.4 9.7 + - - +
273A ARG* 1.3 85.1 - - - +
275A LEU* 1.3 67.9 + - - +
276A LEU 3.1 1.0 + - - -
277A ASP* 3.0 30.8 + - - +
278A ALA* 3.0 22.6 + - - +
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Residues in contact with LEU 275 (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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140A MET 4.0 4.7 - - - +
141A VAL* 3.9 26.7 - - + -
144A ALA* 3.5 31.6 - - + +
195A LEU* 3.2 20.2 + - + +
196A CYS* 4.1 11.7 - - + -
274A ASP* 1.3 76.6 - - - +
276A LEU* 1.3 62.7 + - - +
278A ALA* 3.4 3.2 - - + +
279A LEU* 3.2 39.4 + - + +
306A THR* 5.0 0.2 - - + -
307A VAL* 4.5 11.0 - - + -
310A ILE* 3.9 39.0 - - + -
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Residues in contact with LEU 276 (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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196A CYS 3.2 15.3 + - - +
197A PHE* 3.8 30.1 - - + -
256A LEU 5.4 0.4 - - - +
259A LYS* 3.9 24.2 - - + +
260A TYR* 4.2 14.1 - - + +
263A HIS* 3.9 19.1 - - + +
274A ASP* 3.0 5.5 - - - +
275A LEU* 1.3 75.3 - - - +
277A ASP* 1.3 62.2 + - - +
279A LEU* 2.9 3.3 + - - -
280A LEU* 2.8 35.9 + - + +
303A VAL* 3.8 27.8 - - + -
304A LEU* 5.9 3.1 - - + -
307A VAL* 4.3 12.9 - - + +
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Residues in contact with ASP 277 (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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263A HIS* 3.3 10.6 + - - +
267A TYR* 3.8 26.6 + - + -
268A SER 4.9 0.5 + - - +
271A VAL* 4.0 5.4 - - - +
272A GLN* 3.8 12.9 - - + -
273A ARG* 2.8 66.1 + - - +
274A ASP* 3.0 17.3 + - - +
276A LEU* 1.3 75.3 - - - +
278A ALA* 1.3 62.8 + - - +
280A LEU* 3.7 3.8 - - - +
281A ARG* 2.9 27.8 + - - +
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Residues in contact with ALA 278 (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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140A MET* 4.1 13.1 - - - +
144A ALA* 4.3 10.3 - - + -
272A GLN* 3.7 27.7 - - - +
274A ASP 3.0 12.4 + - - +
275A LEU* 3.4 18.8 - - + +
277A ASP* 1.3 77.3 - - - +
279A LEU* 1.3 57.4 + - + +
281A ARG* 3.6 6.1 - - - +
282A ALA* 3.2 23.2 + - - +
150B GLU* 5.8 0.3 - - - +
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Residues in contact with LEU 279 (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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137A HIS* 4.2 21.8 - - + +
140A MET* 3.8 31.0 - - + -
275A LEU* 3.4 28.3 - - + +
276A LEU* 2.9 5.4 + - - +
278A ALA* 1.3 76.8 - - - +
280A LEU* 1.3 66.7 + - - +
281A ARG 3.1 1.6 - - - -
282A ALA* 3.3 4.9 - - - +
283A LYS* 2.9 23.9 + - - +
298A LEU* 4.8 8.4 - - + +
303A VAL* 4.1 31.9 - - + +
306A THR* 4.2 9.6 - - + -
307A VAL* 3.6 28.3 - - + -
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Residues in contact with LEU 280 (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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260A TYR* 3.7 35.4 - - + +
263A HIS* 3.9 28.3 - - + -
264A LYS* 4.1 26.9 - - + +
267A TYR* 4.3 21.5 - - + -
276A LEU* 2.8 27.7 + - + +
277A ASP* 3.7 7.6 - - - +
279A LEU* 1.3 76.4 - - - +
281A ARG* 1.3 58.3 + - - +
283A LYS* 3.1 14.7 + - + +
284A ARG* 3.0 34.9 + - - +
303A VAL* 5.1 2.2 - - + -
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Residues in contact with ARG 281 (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* 3.3 22.8 + - - +
269A ASP* 3.8 21.2 + - - -
270A ASN 4.2 5.5 + - - -
271A VAL 4.0 4.8 + - - -
272A GLN* 3.5 41.4 + - - +
277A ASP 2.9 18.1 + - - +
278A ALA* 3.6 6.1 - - - +
280A LEU* 1.3 73.9 - - - +
282A ALA* 1.3 66.8 + - - +
283A LYS 3.2 0.2 + - - -
284A ARG* 3.3 10.6 + - - +
285A SER* 3.2 28.7 + - - +
147B MET* 6.0 3.2 - - - -
150B GLU* 5.6 11.2 + - - +
269B ASP 5.1 5.5 + - - +
272B GLN* 6.2 1.4 - - - +
281B ARG* 3.7 38.3 - - - +
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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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136A PHE* 4.5 5.6 - - + -
140A MET* 4.0 21.5 - - + -
278A ALA 3.2 11.7 + - - +
279A LEU* 3.3 11.4 - - - +
281A ARG* 1.3 80.9 - - - +
283A LYS* 1.3 62.4 + - - +
285A SER* 3.3 7.9 + - - -
286A SER 3.1 17.8 + - - -
298A LEU* 3.6 25.3 - - + +
150B GLU* 5.6 5.4 - - - +
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Residues in contact with LYS 283 (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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260A TYR* 3.9 21.3 - - - +
264A LYS* 6.0 1.3 - - - -
279A LEU 2.9 14.4 + - - +
280A LEU* 3.1 18.4 + - + +
282A ALA* 1.3 73.2 - - - +
284A ARG* 1.3 68.0 + - - +
286A SER* 3.2 15.4 + - - -
287A GLU* 3.5 4.2 + - - +
298A LEU* 3.1 36.9 + - + +
299A THR* 3.9 3.1 - - - +
300A GLU* 3.7 23.8 - - - +
303A VAL* 4.4 10.3 - - + -
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Residues in contact with ARG 284 (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* 2.8 49.5 + - - -
269A ASP* 4.2 15.5 + - - -
280A LEU* 3.0 19.2 + - - +
281A ARG* 3.8 9.1 + - - +
283A LYS* 1.3 75.2 - - - +
285A SER* 1.3 56.3 + - - +
287A GLU* 2.7 41.5 + - + +
288A ASN* 3.6 10.9 + - - +
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Residues in contact with SER 285 (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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281A ARG* 3.2 15.5 + - - +
282A ALA* 3.4 12.3 - - - -
284A ARG* 1.3 80.5 - - - +
286A SER* 1.3 60.5 + - - +
287A GLU 3.2 0.2 - - - -
288A ASN* 3.4 30.5 + - - +
289A ASN* 3.9 4.9 + - - +
269B ASP 5.4 0.2 + - - -
270B ASN* 3.5 22.6 + - - -
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Residues in contact with SER 286 (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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282A ALA 3.1 11.3 + - - -
283A LYS* 3.4 11.2 - - - -
284A ARG 3.1 0.6 + - - -
285A SER* 1.3 76.3 - - - +
287A GLU* 1.3 62.1 + - - +
289A ASN* 3.3 22.2 + - - +
295A ASP 5.7 2.3 + - - -
296A VAL 5.0 5.9 + - - -
298A LEU* 4.2 21.4 - - - +
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Residues in contact with GLU 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 LYS 3.5 4.6 + - - +
284A ARG* 2.7 25.1 + - + +
286A SER* 1.3 73.1 - - - +
288A ASN* 1.3 89.5 + - - +
289A ASN 3.3 6.8 + - - +
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Residues in contact with ASN 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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284A ARG* 3.6 9.1 - - - +
285A SER* 3.4 25.7 + - - +
286A SER 3.3 0.6 - - - -
287A GLU* 1.3 107.0 - - - +
289A ASN* 1.3 60.1 + - - +
270B ASN* 3.1 27.9 + - - +
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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