Contacts of the helix formed by residues 269 - 280 (chain B) in PDB entry 3LEE
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 HIS 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASP* 4.9 3.6 + - - -
206B SER* 3.0 45.3 - - - +
209B LEU* 3.2 23.8 - - + +
210B PHE* 4.2 13.3 + - + -
213B LYS* 3.1 44.3 + - + +
265B ASN* 4.1 5.4 + - - -
266B ALA 3.1 17.8 + - - +
267B LEU 2.9 1.0 - - - -
268B HIS* 1.3 79.5 - - + +
270B ILE* 1.3 65.9 + - - +
271B PRO* 3.0 4.2 - - - -
272B ASP* 3.2 10.7 + - - +
273B VAL* 3.1 18.8 + - - +
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Residues in contact with ILE 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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210B PHE* 3.3 39.0 - - + -
267B LEU* 3.0 25.1 + - + +
269B HIS* 1.3 77.9 - - - +
271B PRO* 1.3 62.0 - - + +
273B VAL* 2.7 30.2 + - + +
274B ILE* 2.8 37.5 + - + -
297B ILE* 3.6 22.2 - - + -
338B ILE* 4.2 13.2 - - + -
342B MET* 4.8 2.9 - - - -
366B ILE* 3.9 20.9 - - + -
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Residues in contact with PRO 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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267B LEU 3.9 1.6 - - - +
268B HIS* 3.3 16.4 - - - +
269B HIS 3.3 4.0 - - - -
270B ILE* 1.3 98.6 - - + +
272B ASP* 1.3 55.2 + - - +
274B ILE* 3.3 10.3 + - + +
275B THR* 2.7 32.8 + - - -
362B ILE* 4.9 2.9 - - + -
365B THR* 4.7 5.8 - - + -
366B ILE* 4.0 18.4 - - + -
369B GLN* 4.2 34.1 - - + +
370B ASN 6.2 0.2 - - - -
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Residues in contact with ASP 272 (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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202B GLU* 4.2 6.9 - - - +
203B ARG* 2.9 36.0 + - - +
206B SER* 2.5 40.3 + - - -
268B HIS 5.2 1.0 + - - +
269B HIS* 3.2 7.4 + - - +
271B PRO* 1.3 76.8 - - - +
273B VAL* 1.3 58.7 + - - +
275B THR* 3.0 6.4 + - - -
276B TYR* 2.8 31.7 + - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER 4.4 15.0 - - - +
207B MET* 3.7 16.8 - - - -
210B PHE* 4.5 10.1 - - + -
269B HIS 3.1 17.9 + - - +
270B ILE* 2.7 28.4 + - + +
272B ASP* 1.3 72.6 - - - +
274B ILE* 1.3 59.3 + - + +
276B TYR* 3.4 1.0 + - - +
277B LEU* 3.1 44.3 + - + +
293B GLN* 3.7 32.3 - - + +
297B ILE* 5.8 1.3 - - + -
338B ILE* 5.6 5.8 - - + -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 2.8 37.6 + - + +
271B PRO* 3.8 10.3 - - + +
272B ASP 3.2 0.2 - - - -
273B VAL* 1.3 72.3 - - + +
275B THR* 1.3 63.4 + - - +
277B LEU* 4.9 1.3 - - - -
278B SER* 2.9 11.1 + - - +
331B MET* 2.8 38.8 - - + +
335B LYS* 4.1 24.7 - - + -
338B ILE* 4.3 23.8 - - + -
339B TYR* 4.5 26.0 - - + +
366B ILE* 5.1 5.6 - - + +
369B GLN* 6.2 2.5 - - + -
370B ASN* 4.7 14.6 - - - +
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Residues in contact with THR 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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203B ARG* 3.4 37.6 + - - +
271B PRO 2.7 23.2 + - - -
272B ASP* 3.4 5.8 + - - -
274B ILE* 1.3 76.0 - - - +
276B TYR* 1.3 66.5 + - - +
278B SER* 2.6 21.2 + - - +
279B ARG* 3.4 28.7 - - - +
370B ASN* 4.9 12.3 + - - +
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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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183B LEU* 5.6 0.2 - - - +
184B SER* 2.8 28.5 + - - -
187B PHE* 3.6 18.9 - - - -
197B VAL* 3.5 28.6 - - + +
200B ASP 5.8 0.2 - - - -
203B ARG* 4.2 10.3 - - + +
204B ALA* 4.0 22.0 - - + -
207B MET* 3.7 37.7 - - + -
272B ASP 2.8 19.4 + - - +
273B VAL 3.7 4.3 - - - +
275B THR* 1.3 73.5 - - - +
277B LEU* 1.3 69.6 + - - +
279B ARG* 2.9 28.1 + - - +
280B LEU* 3.6 17.0 + - + +
289B CYS* 3.9 21.9 - - - -
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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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207B MET* 4.4 7.4 - - + -
273B VAL* 3.1 38.0 + - + +
274B ILE* 5.2 0.4 - - - -
276B TYR* 1.3 81.5 - - - +
278B SER* 1.3 64.2 + - - +
279B ARG 3.2 0.5 + - - -
280B LEU* 3.3 27.7 + - + +
286B PHE* 3.7 17.4 - - + -
289B CYS* 3.8 14.8 - - + -
290B ALA* 3.5 36.8 - - + +
293B GLN* 4.4 13.5 - - + -
331B MET* 3.6 19.5 - - + -
334B VAL* 4.4 19.3 - - + -
338B ILE* 5.4 2.0 - - + -
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Residues in contact with SER 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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274B ILE* 2.9 17.5 + - - +
275B THR* 2.6 27.7 + - - +
277B LEU* 1.3 78.8 - - - +
279B ARG* 1.3 57.3 + - - +
280B LEU 3.5 1.4 + - - +
281B ARG* 2.9 27.4 + - - -
331B MET* 3.2 23.6 - - - +
335B LYS* 6.2 1.1 - - - -
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 3.9 3.1 - - - +
194B ASP* 5.3 4.6 - - + +
196B LEU* 3.4 37.0 + - + +
197B VAL* 4.6 21.2 - - + +
200B ASP* 3.0 37.2 + - - +
203B ARG* 3.6 27.3 - - - +
275B THR* 3.4 29.9 - - + +
276B TYR* 2.9 14.3 + - - +
278B SER* 1.3 77.7 - - - +
280B LEU* 1.3 66.1 + - - +
281B ARG* 3.5 26.1 + - - +
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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
----------------------------------------------------------
187B PHE* 4.6 1.3 - - + -
193B GLU* 3.5 24.7 - - + +
197B VAL* 4.7 7.4 - - + -
276B TYR* 3.6 28.0 + - + +
277B LEU* 3.3 26.8 + - + +
278B SER 3.7 2.4 - - - +
279B ARG* 1.3 80.1 - - - +
281B ARG* 1.3 70.7 + - - +
282B ASN 3.6 0.4 - - - -
285B VAL* 3.6 15.9 - - + +
286B PHE* 3.7 38.0 - - + -
289B CYS* 3.7 24.9 - - + -
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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