Contacts of the helix formed by residues 268 - 278 (chain C) in PDB entry 3TQI
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 ASN 268 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C ARG* 3.2 1.0 - - - +
267C LEU* 1.3 104.0 + - - +
269C GLU* 1.3 57.7 + - - +
270C VAL 3.4 2.5 - - - -
271C ASP* 3.5 23.5 + - + +
272C GLU* 2.9 49.7 + - + +
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Residues in contact with GLU 269 (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 SER* 6.5 0.7 - - - -
237C GLY* 5.1 11.8 + - - -
265C LEU* 4.1 27.2 - - + +
266C ARG* 3.2 44.7 + - - +
267C LEU 4.0 0.2 + - - -
268C ASN* 1.3 77.6 - - - +
270C VAL* 1.3 64.6 + - - +
272C GLU* 3.2 13.0 + - + +
273C VAL* 3.0 32.8 + - + +
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Residues in contact with VAL 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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259C LEU* 4.2 17.7 - - + -
261C ASP* 3.8 38.1 - - + +
265C LEU* 4.5 11.6 - - + +
266C ARG 4.9 0.4 + - - -
267C LEU 5.4 0.2 + - - -
268C ASN 3.4 0.4 - - - -
269C GLU* 1.3 76.5 - - - +
271C ASP* 1.3 69.5 + - - +
273C VAL* 3.0 22.5 - - - +
274C LEU* 3.0 24.5 + - + +
287C CYS* 5.3 4.9 - - - -
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Residues in contact with ASP 271 (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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267C LEU 5.3 1.0 - - - +
268C ASN* 3.5 26.0 + - + +
269C GLU 3.3 0.4 - - - -
270C VAL* 1.3 85.3 - - - +
272C GLU* 1.3 64.4 - - + +
274C LEU* 3.1 11.3 + - - +
275C ASN* 2.9 33.8 + - - +
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Residues in contact with GLU 272 (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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268C ASN* 2.9 41.3 + - + +
269C GLU* 3.8 14.9 - - + +
271C ASP* 1.3 73.4 - - + +
273C VAL* 1.3 61.2 + - - +
275C ASN* 3.4 11.7 + - - +
276C VAL* 3.4 26.6 + - - +
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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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234C LEU* 3.7 35.7 - - + +
259C LEU* 3.3 27.1 - - + -
269C GLU* 3.0 24.5 + - + +
270C VAL* 3.0 15.7 - - - +
272C GLU* 1.3 74.6 - - - +
274C LEU* 1.3 66.3 + - + +
276C VAL* 3.3 6.8 + - - +
277C PHE* 3.0 43.0 + - + +
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Residues in contact with LEU 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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234C LEU* 6.3 0.4 - - + -
259C LEU* 4.1 13.0 - - + -
270C VAL* 3.0 33.9 + - + +
271C ASP* 3.1 10.3 + - - +
273C VAL* 1.3 77.7 - - - +
275C ASN* 1.3 60.1 + - - +
277C PHE* 5.2 0.7 - - - -
278C GLN* 2.7 64.2 + - + +
279C LYS* 3.3 6.9 + - - -
285C VAL* 4.1 17.0 - - + -
287C CYS* 4.0 26.2 - - - -
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Residues in contact with ASN 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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129A VAL* 3.8 9.8 - - + +
130A SER 3.6 14.3 + - - +
131A PRO* 3.4 40.1 - - - +
133A GLY* 3.9 0.9 - - - -
271C ASP* 2.9 25.5 + - - +
272C GLU* 3.5 13.6 - - - +
273C VAL 3.2 0.4 - - - -
274C LEU* 1.3 78.1 - - - +
276C VAL* 1.3 56.9 + - - +
279C LYS* 3.4 24.7 + - + +
280C HIS* 3.0 28.9 + - - +
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Residues in contact with VAL 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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129A VAL* 3.6 35.2 - - + -
272C GLU 3.4 13.2 - - - +
273C VAL* 3.3 8.0 + - - +
275C ASN* 1.3 75.9 - - - +
277C PHE* 1.3 90.8 + - + +
280C HIS* 2.6 30.7 - - - +
281C LEU* 3.3 15.6 - - + +
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Residues in contact with PHE 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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234C LEU* 3.8 31.4 - - + -
241C ALA* 3.5 39.7 - - + -
244C ALA* 3.8 15.0 - - + -
245C THR* 3.4 25.1 - - + -
255C LEU* 6.2 0.4 - - + -
257C CYS* 4.7 6.3 - - - -
273C VAL* 3.0 27.8 + - + +
274C LEU* 5.2 0.4 - - - -
276C VAL* 1.3 109.0 - - + +
278C GLN* 1.3 52.6 + - - +
280C HIS 3.5 4.7 - - - +
281C LEU* 3.6 16.5 - - + +
282C GLY 2.6 23.4 - - - +
283C ALA* 2.7 18.6 - - + +
285C VAL* 4.4 7.0 - - + -
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Residues in contact with GLN 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 LEU* 2.7 53.1 + - + +
277C PHE* 1.3 73.3 - - - +
279C LYS* 1.3 73.9 + - + +
282C GLY* 2.7 20.9 - - - +
283C ALA 4.3 10.3 - - - +
285C VAL* 4.2 24.5 + - + +
287C CYS* 5.9 0.4 - - - -
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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