Contacts of the helix formed by residues 269 - 278 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C ASP* 4.9 3.0 + - - -
206C SER* 4.1 21.1 - - - +
209C LEU* 3.5 31.7 - - + +
210C PHE* 3.8 27.8 + - + -
213C LYS* 3.0 42.4 + - + +
265C ASN 4.2 4.7 + - - -
266C ALA* 3.3 20.3 + - - +
267C LEU 2.8 1.4 + - - -
268C HIS* 1.3 80.5 - - + +
270C ILE* 1.3 64.7 + - - +
271C PRO* 3.2 0.7 - - - -
272C ASP* 2.9 19.5 + - - +
273C VAL* 2.9 12.7 + - - +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C PHE* 3.6 24.0 - - + -
267C LEU* 2.8 23.1 + - + +
269C HIS* 1.3 75.6 - - - +
271C PRO* 1.3 63.1 - - + +
273C VAL* 2.7 33.6 + - + +
274C ILE* 2.7 31.2 + - + -
297C ILE* 3.6 30.3 - - + -
338C ILE* 4.1 16.4 - - + -
342C MET* 4.4 13.2 - - + -
366C ILE* 3.7 20.9 - - + -
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Residues in contact with PRO 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ARG* 5.2 0.4 + - - -
267C LEU 4.0 1.1 - - - +
268C HIS* 3.1 20.2 - - - +
269C HIS 3.2 1.6 - - - -
270C ILE* 1.3 96.8 - - + +
272C ASP* 1.3 56.4 + - - +
274C ILE* 3.8 5.8 - - + -
275C THR* 2.9 29.5 + - - -
362C ILE* 4.7 5.8 - - + -
365C THR* 5.2 1.8 - - - +
366C ILE* 4.1 20.0 - - + +
369C GLN* 3.4 28.0 - - + +
370C ASN* 3.7 14.9 + - - +
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Residues in contact with ASP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU* 3.9 8.8 - - - +
203C ARG* 2.8 42.1 + - + +
206C SER* 2.6 34.7 + - - +
268C HIS 5.5 0.4 - - - +
269C HIS* 2.9 12.4 + - - +
271C PRO* 1.3 78.5 - - - +
273C VAL* 1.3 65.6 + - - +
274C ILE 3.1 1.3 - - - -
275C THR* 3.4 3.8 + - - +
276C TYR* 3.0 24.4 + - - +
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C SER* 4.5 2.0 - - - +
207C MET* 3.7 25.1 - - - +
210C PHE* 4.0 35.0 - - + -
269C HIS 2.9 15.1 + - - +
270C ILE* 2.7 20.9 + - + +
272C ASP* 1.3 72.8 - - - +
274C ILE* 1.3 58.4 + - + +
276C TYR* 3.6 2.4 - - - +
277C LEU* 3.1 36.1 + - + +
293C GLN* 3.8 32.8 - - + +
297C ILE* 5.7 2.7 - - + -
338C ILE* 5.6 4.3 - - + -
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ILE* 2.7 34.1 + - + +
271C PRO* 3.9 7.2 - - + +
273C VAL* 1.3 73.4 - - + +
275C THR* 1.3 66.4 + - - +
277C LEU* 3.3 3.9 + - - +
278C SER* 3.1 25.5 + - - -
331C MET* 3.9 20.5 - - + +
335C LYS* 4.3 10.5 - - + -
338C ILE* 3.8 35.2 - - + -
339C TYR* 4.2 21.3 - - + +
366C ILE* 5.2 3.4 - - + +
370C ASN* 3.8 29.4 - - + +
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Residues in contact with THR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ARG* 3.7 40.0 + - + +
271C PRO 2.9 19.1 + - - -
272C ASP 3.8 4.3 - - - -
274C ILE* 1.3 76.2 - - - +
276C TYR* 1.3 63.6 + - - +
278C SER* 2.8 20.0 + - - +
279C ARG* 3.5 30.0 - - + +
370C ASN* 3.4 16.9 + - - +
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Residues in contact with TYR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LEU* 5.6 0.3 - - - +
184C SER* 2.6 30.2 + - - -
187C PHE* 3.8 14.7 - - - -
197C VAL* 3.5 30.3 - - + +
200C ASP 5.5 0.4 - - - -
203C ARG* 4.2 10.0 - - + +
204C ALA* 4.0 26.7 - - + -
207C MET* 3.7 32.3 - - + -
272C ASP 3.0 17.5 + - - +
273C VAL 3.6 5.2 - - - +
275C THR* 1.3 76.8 - - - +
277C LEU* 1.3 70.9 + - + +
279C ARG* 2.9 28.5 + - - +
280C LEU* 3.8 13.9 + - + +
289C CYS* 4.0 22.0 - - - -
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C MET* 4.0 10.1 - - + -
273C VAL* 3.1 30.3 + - + +
274C ILE* 3.3 3.3 + - - +
276C TYR* 1.3 81.7 - - + +
278C SER* 1.3 57.5 + - - +
279C ARG 3.0 4.6 + - - -
280C LEU* 3.2 24.2 + - + +
286C PHE* 3.6 16.0 - - + +
289C CYS* 3.7 41.1 - - + +
290C ALA* 3.8 17.5 - - + +
293C GLN* 4.9 4.3 - - + -
294C VAL* 5.9 0.2 - - + -
331C MET* 3.7 15.0 - - + -
334C VAL* 4.0 26.7 - - + -
338C ILE* 5.2 2.5 - - + -
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 3.1 15.7 + - - -
275C THR* 2.8 24.9 + - - +
276C TYR 3.0 0.2 + - - -
277C LEU* 1.3 75.9 - - - +
279C ARG* 1.3 57.9 + - - +
280C LEU 3.5 1.3 - - - -
281C ARG* 3.3 15.7 + - - -
331C MET* 3.5 26.2 - - - -
335C LYS* 6.0 0.7 - - - -
370C ASN* 4.9 3.4 + - - -
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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