Contacts of the helix formed by residues 274 - 289 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA 5.7 0.2 - - - -
148B PHE* 4.3 5.4 - - - -
194B ALA 3.8 5.2 - - - +
195B LEU 3.2 13.9 - - - +
196B CYS 3.1 11.2 - - - +
197B PHE 2.7 29.5 - - - +
198B ASN* 2.8 14.8 + - + +
263B HIS* 2.8 19.8 + - - -
272B GLN* 3.7 11.3 - - - +
273B ARG* 1.3 79.6 - - - +
275B LEU* 1.3 66.2 + - - +
276B LEU 3.2 3.3 + - - -
277B ASP* 3.2 25.5 + - - +
278B ALA* 3.2 7.6 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET 4.0 3.1 - - - +
141B VAL* 3.8 26.0 - - + +
144B ALA* 3.5 30.9 + - + +
148B PHE* 6.0 0.2 - - - +
195B LEU* 2.9 31.4 + - + +
196B CYS* 4.1 18.4 - - - -
274B ASP* 1.3 71.1 - - - +
276B LEU* 1.3 65.5 + - - +
278B ALA* 2.9 17.2 + - + +
279B LEU* 2.9 28.4 + - + +
306B THR* 5.2 0.2 - - + -
307B VAL* 4.3 16.8 - - + +
310B ILE* 4.0 26.5 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B CYS 3.4 12.8 + - - +
197B PHE* 4.1 19.1 - - + -
256B LEU 5.5 0.4 - - - +
259B LYS* 4.4 0.2 - - + -
260B TYR* 4.2 31.4 - - + +
263B HIS* 3.6 41.1 - - + +
274B ASP* 3.2 4.4 + - - +
275B LEU* 1.3 81.4 - - - +
277B ASP* 1.3 58.2 + - - +
279B LEU* 3.0 7.8 + - - +
280B LEU* 2.8 33.1 + - + +
303B VAL* 4.2 17.0 - - + +
304B LEU* 5.5 4.0 - - + -
307B VAL* 3.9 23.3 - - + +
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Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B HIS* 3.1 21.1 + - - +
267B TYR* 3.2 30.1 - - + -
268B SER 5.0 0.2 - - - +
271B VAL 3.7 9.4 - - - +
272B GLN* 4.3 5.8 - - - -
273B ARG* 2.8 54.1 + - - +
274B ASP* 3.2 13.8 + - - +
276B LEU* 1.3 76.2 - - - +
278B ALA* 1.3 63.9 + - - +
280B LEU* 3.1 10.5 + - - +
281B ARG* 2.9 24.9 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 4.9 8.5 - - + -
140B MET* 4.7 6.9 - - + +
144B ALA* 3.9 15.9 - - + -
272B GLN* 3.6 32.0 - - - +
274B ASP 3.2 3.2 + - - +
275B LEU* 2.9 14.4 + - + +
277B ASP* 1.3 79.6 - - - +
279B LEU* 1.3 60.7 + - + +
281B ARG* 3.5 8.7 + - - +
282B ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B HIS* 4.1 22.7 - - + +
140B MET* 4.0 28.9 - - + -
275B LEU* 2.9 26.2 + - + +
276B LEU 3.0 7.2 + - - +
278B ALA* 1.3 76.2 - - - +
280B LEU* 1.3 65.8 + - - +
282B ALA* 3.5 3.8 + - - +
283B LYS* 3.0 22.9 + - - +
298B LEU* 4.5 10.4 - - + +
303B VAL* 3.9 26.4 - - + +
306B THR* 4.1 16.8 - - + -
307B VAL* 3.7 30.3 - - + -
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Residues in contact with LEU 280 (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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260B TYR* 3.6 37.7 - - + +
263B HIS* 3.9 29.8 - - + -
264B LYS* 4.1 26.7 - - + +
267B TYR* 4.5 17.7 - - + -
276B LEU* 2.8 21.7 + - + +
277B ASP* 3.4 14.1 - - - +
279B LEU* 1.3 75.6 - - - +
281B ARG* 1.3 51.9 + - - +
283B LYS* 2.7 16.7 + - + +
284B ARG* 2.7 36.6 + - - +
303B VAL* 5.0 3.8 - - + -
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASP 4.7 2.4 + - - -
270A ASN 4.7 6.3 - - - +
281A ARG* 3.7 40.8 - - - +
267B TYR* 3.6 30.9 + - - +
269B ASP* 3.4 50.8 + - - +
271B VAL 3.3 29.1 + - - -
272B GLN* 4.0 11.5 + - - +
277B ASP 2.9 11.4 + - - +
278B ALA* 3.6 11.5 - - - +
280B LEU* 1.3 74.4 - - - +
282B ALA* 1.3 53.4 + - - +
284B ARG* 3.3 5.0 + - + +
285B SER* 2.7 46.9 + - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.0 17.4 - - + -
140B MET* 3.8 24.7 - - + -
278B ALA 3.2 14.0 + - - +
279B LEU* 3.8 5.8 - - - +
280B LEU 3.2 0.6 - - - -
281B ARG* 1.3 80.0 - - - +
283B LYS* 1.3 57.9 + - - +
285B SER* 3.5 8.4 + - - -
286B SER* 3.1 26.2 + - - -
298B LEU* 3.7 8.6 - - + +
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TYR* 3.9 20.7 + - - +
279B LEU 3.0 13.6 + - - +
280B LEU* 2.7 22.0 + - + +
282B ALA* 1.3 70.2 - - - +
284B ARG* 1.3 64.8 + - - +
286B SER* 3.2 14.3 + - - -
287B GLU* 3.3 41.5 + - - +
298B LEU* 3.5 35.8 - - + +
299B THR* 4.0 2.8 - - - +
300B GLU* 3.6 26.3 + - - +
303B VAL* 4.2 7.6 - - + -
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 4.8 8.3 - - - +
267B TYR* 3.3 38.9 - - + -
268B SER* 4.8 4.6 + - - +
269B ASP* 2.7 40.5 + - - +
280B LEU 2.7 18.5 + - - +
281B ARG* 3.8 4.3 - - + +
283B LYS* 1.3 73.0 - - - +
285B SER* 1.3 67.4 + - - +
286B SER 3.2 0.5 + - - -
287B GLU* 3.3 11.6 + - - +
288B ASN* 3.1 37.5 + - - +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 3.4 43.1 + - - +
271A VAL* 6.1 2.0 - - - -
281B ARG* 2.7 30.5 + - - +
282B ALA* 3.5 9.1 - - - -
284B ARG* 1.3 74.6 - - - +
286B SER* 1.3 63.8 + - - +
288B ASN* 3.5 13.2 + - - +
289B ASN* 3.8 8.0 + - - +
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Residues in contact with SER 286 (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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282B ALA 3.1 14.1 + - - -
283B LYS* 3.4 10.1 - - - -
284B ARG 3.2 0.6 - - - -
285B SER* 1.3 76.0 - - - +
287B GLU* 1.3 65.6 + - - +
289B ASN* 3.2 24.6 + - - +
296B VAL 5.3 2.1 + - - -
298B LEU* 3.9 23.1 - - - +
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Residues in contact with GLU 287 (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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283B LYS* 3.3 53.7 + - - +
284B ARG* 3.3 9.3 + - - +
286B SER* 1.3 81.7 + - - +
288B ASN* 1.3 64.6 + - - +
289B ASN 3.1 6.6 + - - +
298B LEU* 6.0 0.3 - - - +
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Residues in contact with ASN 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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270A ASN* 3.3 33.6 + - - +
284B ARG* 3.1 28.5 + - - +
285B SER 3.7 2.0 - - - +
286B SER 3.3 1.0 - - - -
287B GLU* 1.3 79.7 - - - +
289B ASN* 1.3 58.6 + - - +
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Residues in contact with ASN 289 (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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285B SER 3.8 6.9 + - - +
286B SER* 3.2 17.4 + - - +
287B GLU* 3.1 6.8 - - - +
288B ASN* 1.3 82.2 - - + +
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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