Contacts of the helix formed by residues 276 - 286 (chain C) in PDB entry 2Z9I
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 SER 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PRO* 5.4 1.7 - - - +
237C ASN* 3.1 23.3 - - - +
243C GLY* 3.8 4.0 - - - -
244C ALA* 3.4 9.8 - - - +
274C ILE* 3.3 20.7 + - - +
275C ASN* 1.3 80.1 - - - +
277C ALA* 1.3 65.7 + - - +
278C ASP* 3.7 9.5 + - - +
279C ALA* 3.4 22.3 + - - +
280C LEU 3.5 0.2 + - - -
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Residues in contact with ALA 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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235C VAL* 3.7 22.7 - - + +
236C THR* 3.6 13.2 - - - +
237C ASN* 3.3 21.9 + - - +
244C ALA* 3.8 12.6 - - - +
276C SER* 1.3 73.6 - - - +
278C ASP* 1.3 68.7 + - - +
280C LEU* 3.3 6.1 + - - +
281C VAL* 3.0 28.3 + - + +
2I ALA* 6.3 0.2 - - - -
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Residues in contact with ASP 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PRO* 3.7 16.2 - - + +
143C SER* 2.9 26.8 + - - +
154C VAL* 3.7 12.7 - - + +
276C SER* 3.4 9.0 + - - +
277C ALA* 1.3 80.3 - - - +
279C ALA* 1.3 56.7 + - - +
281C VAL* 4.3 7.6 - - - +
282C ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PRO* 3.7 22.1 - - + +
273C PRO 5.3 0.7 - - - +
274C ILE* 3.5 27.9 - - + +
275C ASN* 3.6 13.7 - - + +
276C SER* 3.4 16.0 + - - +
277C ALA 3.2 0.8 - - - -
278C ASP* 1.3 79.4 - - - +
280C LEU* 1.3 57.1 + - - +
282C ALA* 3.8 1.6 - - - +
283C ALA* 3.0 29.8 + - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 3.9 26.7 - - + -
233C VAL* 4.3 0.7 - - + -
235C VAL* 4.0 11.9 - - + -
244C ALA* 3.8 28.0 - - + -
266C VAL* 4.1 20.0 - - + -
269C VAL* 3.8 25.6 - - + -
274C ILE* 4.0 7.3 - - + +
276C SER 3.5 1.6 + - - -
277C ALA 3.3 8.3 + - - +
279C ALA* 1.3 76.5 - - - +
281C VAL* 1.3 65.4 + - - +
283C ALA* 3.3 2.9 + - - +
284C VAL* 3.0 36.9 + - + +
4I VAL* 3.9 24.0 - - + -
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C VAL* 4.2 21.9 - - + +
235C VAL* 4.5 8.5 - - + -
277C ALA* 3.0 21.6 + - + +
278C ASP* 3.8 9.6 - - - +
280C LEU* 1.3 76.2 - - - +
282C ALA* 1.3 64.0 + - - +
284C VAL* 3.6 1.2 + - - +
285C ARG* 3.4 49.5 + - - +
2I ALA* 5.4 3.4 - - - +
3I THR 4.7 7.2 - - - +
4I VAL* 3.9 30.3 - - + +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PRO* 3.8 22.2 - - + -
154C VAL* 3.8 12.9 - - + +
155C LEU 3.8 15.9 - - - +
156C ASP* 3.6 20.2 - - + +
278C ASP 2.8 21.6 + - - +
279C ALA 3.8 4.3 - - - +
281C VAL* 1.3 71.7 - - - +
283C ALA* 1.3 57.2 + - - +
285C ARG* 3.0 20.0 + - - +
286C SER 3.1 10.0 + - - -
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Residues in contact with ALA 283 (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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156C ASP* 4.8 4.0 - - - -
269C VAL* 4.4 31.2 - - + +
272C ARG* 6.0 4.7 - - + -
274C ILE* 4.7 4.5 - - + -
279C ALA 3.0 19.1 + - - +
280C LEU 3.3 3.8 + - - +
282C ALA* 1.3 72.6 - - - +
284C VAL* 1.3 65.4 + - + +
286C SER* 3.1 27.2 + - - -
287C LYS* 3.9 3.6 + - - +
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Residues in contact with VAL 284 (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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229C ALA* 3.2 50.2 - - + +
230C SER* 4.3 7.2 - - - +
231C LEU* 4.3 13.5 - - + -
269C VAL* 6.1 3.1 - - + -
280C LEU* 3.0 35.6 + - + +
281C VAL 3.9 1.8 - - - +
283C ALA* 1.3 74.8 - - + +
285C ARG* 1.3 61.3 + - - +
287C LYS* 3.3 13.0 + - - +
311C LEU* 4.8 9.9 - - + -
4I VAL* 3.4 29.4 - - + -
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Residues in contact with ARG 285 (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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86C THR* 3.9 31.5 + - - +
87C SER* 6.2 4.5 - - - -
154C VAL* 4.9 18.5 + - - +
156C ASP* 5.7 1.3 - - + +
212C GLN* 3.9 19.4 - - - +
215C ARG* 4.0 9.2 + - - +
228C HIS* 4.4 22.4 + - + +
229C ALA 4.0 18.4 + - - +
281C VAL* 3.4 38.2 + - - +
282C ALA* 3.0 11.7 + - - +
284C VAL* 1.3 82.6 - - - +
286C SER* 1.3 55.0 + - - +
287C LYS 2.8 18.4 + - - +
3I THR 4.5 9.9 + - - -
4I VAL* 5.2 3.4 - - - +
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Residues in contact with SER 286 (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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139C ASN* 4.9 3.3 + - - -
156C ASP* 3.0 28.9 + - - -
212C GLN* 3.7 18.8 + - - +
282C ALA 3.1 6.2 + - - -
283C ALA* 3.1 15.1 + - - -
285C ARG* 1.3 73.0 - - - +
287C LYS* 1.3 57.5 + - - +
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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