Contacts of the helix formed by residues 267 - 280 (chain B) in PDB entry 3SMP
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 VAL 267 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B GLU 4.4 6.5 - - - +
266B GLU* 1.3 78.8 - - - +
268B GLU* 1.3 64.2 + - - +
269B ASN* 4.0 9.6 - - + +
270B LEU* 3.3 14.8 + - + +
271B LYS* 3.2 18.3 + - - +
331B SER* 5.4 1.8 - - - +
332B LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 268 (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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267B VAL* 1.3 70.7 - - - +
269B ASN* 1.3 71.4 + - - +
271B LYS* 3.1 13.4 + - + +
272B SER* 3.0 33.5 + - - +
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Residues in contact with ASN 269 (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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267B VAL* 3.2 7.4 - - + +
268B GLU* 1.3 83.1 - - - +
270B LEU* 1.3 61.0 + - - +
272B SER* 3.2 15.5 + - - -
273B ILE* 3.3 19.4 + - - +
327B LYS 4.4 9.8 - - - +
328B ASN* 3.9 19.2 - - - +
331B SER* 2.9 34.6 + - - +
332B LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 270 (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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236B PHE* 4.0 18.6 - - + +
237B PRO* 3.9 22.4 - - + -
266B GLU* 3.8 25.8 - - + +
267B VAL* 3.3 13.7 + - + +
268B GLU 3.2 0.2 - - - -
269B ASN* 1.3 77.5 - - - +
271B LYS* 1.3 66.2 + - - +
273B ILE* 3.3 3.1 + - + +
274B ARG* 3.0 46.4 + - + +
332B LEU* 3.9 20.7 - - + +
4006B UNX 3.8 24.2 - - - +
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Residues in contact with LYS 271 (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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263B GLU* 2.6 41.0 + - - +
264B GLN 4.6 1.8 + - - -
266B GLU* 3.1 34.2 + - + +
267B VAL 3.2 9.6 + - - +
268B GLU* 3.1 14.7 + - + +
270B LEU* 1.3 81.1 - - + +
272B SER* 1.3 57.3 + - - +
274B ARG* 3.6 10.6 - - - +
275B LYS* 3.1 26.9 + - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.0 23.8 + - - +
269B ASN* 3.2 10.6 + - - -
271B LYS* 1.3 75.2 - - - +
273B ILE* 1.3 54.4 + - - +
274B ARG 3.2 1.6 - - - -
275B LYS* 4.1 5.5 - - - +
276B TYR* 2.7 35.8 + - - +
327B LYS* 5.1 2.6 + - - -
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PRO* 5.1 6.7 - - + -
239B PHE* 4.4 14.1 - - + -
269B ASN 3.3 20.5 + - - +
270B LEU* 3.9 6.5 - - + +
272B SER* 1.3 77.2 - - - +
274B ARG* 1.3 54.8 + - - +
276B TYR* 3.2 7.7 + - + +
277B LEU* 2.8 53.8 + - + +
324B GLY* 6.5 0.2 - - - -
327B LYS* 3.6 47.3 - - + +
329B PHE* 4.6 17.5 - - + -
332B LEU* 4.6 8.1 - - + -
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Residues in contact with ARG 274 (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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236B PHE* 3.5 21.6 - - - +
252B TYR* 3.4 20.1 + - - +
254B GLU* 5.7 4.0 - - + -
255B PRO* 3.9 6.6 - - + +
258B ILE* 2.8 34.2 - - - +
266B GLU* 3.1 34.9 + - - -
270B LEU* 3.0 26.7 + - + +
271B LYS* 3.6 10.8 - - - +
273B ILE* 1.3 79.1 - - - +
275B LYS* 1.3 58.1 + - - +
277B LEU* 3.5 3.5 + - - +
278B THR* 2.7 35.8 + - - +
4006B UNX 2.9 31.1 + - - +
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Residues in contact with LYS 275 (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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271B LYS 3.1 17.6 + - - +
272B SER* 4.1 5.4 - - - +
274B ARG* 1.3 73.9 - - - +
276B TYR* 1.3 65.1 + - - +
278B THR* 4.6 2.9 - - - +
279B SER* 2.3 38.6 + - - +
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Residues in contact with TYR 276 (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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272B SER 2.7 23.6 + - - +
273B ILE* 3.5 8.5 - - + +
275B LYS* 1.3 74.4 - - - +
277B LEU* 1.3 67.9 + - + +
278B THR 3.6 0.2 + - - -
280B ASN* 3.2 48.7 + - - +
282B ALA 5.8 0.7 - - - -
283B TYR* 3.6 42.5 - + - +
284B GLY 4.2 2.8 + - - -
323B MET* 3.7 32.3 - - + +
327B LYS* 3.4 33.9 - - + +
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Residues in contact with LEU 277 (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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239B PHE* 3.4 32.3 - - + -
250B LEU* 5.3 1.6 - - + -
252B TYR* 3.6 47.1 - - + -
273B ILE* 2.8 34.7 + - + +
274B ARG* 3.8 4.0 - - - +
276B TYR* 1.3 80.2 - - + +
278B THR* 1.3 57.5 - - - +
280B ASN 3.1 8.5 - - - +
283B TYR* 2.6 29.5 + - + +
289B ARG* 3.3 7.0 + - - -
308B HIS* 6.0 0.4 - - + -
310B ILE* 3.6 31.4 - - + -
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Residues in contact with THR 278 (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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252B TYR* 4.4 8.3 - - - -
254B GLU* 3.6 36.6 + - - +
274B ARG* 2.7 23.0 + - - +
275B LYS* 4.5 2.7 - - - -
277B LEU* 1.3 78.1 - - - +
279B SER* 1.3 60.3 + - - +
280B ASN 3.5 0.9 - - - -
289B ARG* 3.3 16.8 + - - +
308B HIS* 5.0 8.5 + - + +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 2.3 35.7 + - - +
276B TYR* 4.6 0.2 - - - -
278B THR* 1.3 77.9 - - - +
280B ASN* 1.3 68.1 + - - +
281B THR* 5.7 0.4 - - - +
289B ARG* 4.5 1.1 - - - -
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Residues in contact with ASN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS 4.9 0.4 + - - -
276B TYR* 3.2 48.4 + - - +
277B LEU 3.1 1.0 - - - +
279B SER* 1.3 87.3 + - - +
281B THR* 1.3 59.0 + - - +
282B ALA 3.6 19.0 - - - +
283B TYR* 2.9 25.1 + - + -
289B ARG* 2.9 16.8 + - - -
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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