Contacts of the helix formed by residues 244 - 255 (chain E) in PDB entry 2TEC
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 244 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242E GLY 3.9 1.0 + - - -
243E ARG* 1.3 78.3 - - - +
245E ALA* 1.3 51.3 + - - +
246E SER* 3.1 20.5 + - - -
247E ASN* 3.4 13.1 + - - +
248E ILE* 2.8 34.9 + - - +
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Residues in contact with ALA 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E TRP* 3.6 30.9 - - + +
154E GLY* 3.5 37.3 + - - +
155E SER 4.4 3.8 - - - +
156E VAL* 4.6 2.9 - - - +
244E SER* 1.3 68.2 - - - +
246E SER* 1.3 59.4 + - - +
248E ILE* 3.0 13.7 + - - +
249E ARG* 2.8 31.0 + - - +
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Residues in contact with SER 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E TRP* 3.9 18.7 - - - -
244E SER* 3.1 13.3 + - - -
245E ALA* 1.3 78.3 - - - +
247E ASN* 1.3 59.4 + - - +
249E ARG* 3.7 3.4 + - - +
250E ALA* 3.1 25.6 + - - +
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Residues in contact with ASN 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E ARG* 2.9 48.8 + - - +
244E SER* 3.3 21.0 + - - +
246E SER* 1.3 79.8 + - - +
248E ILE* 1.3 64.8 + - - +
249E ARG 3.3 0.2 - - - -
250E ALA* 3.7 5.8 - - - +
251E ALA* 3.0 21.7 + - - +
279E TYR* 3.9 16.1 - - - -
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Residues in contact with ILE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LYS* 5.0 4.3 - - + +
154E GLY 5.8 1.6 - - - +
156E VAL* 4.2 16.6 - - + +
235E ALA* 3.8 35.2 - - + +
238E LEU* 3.8 11.2 - - + +
239E ALA* 3.7 39.3 - - + +
243E ARG* 3.9 18.2 - - + +
244E SER 2.8 28.2 + - - +
245E ALA* 3.0 10.7 + - - +
247E ASN* 1.3 74.0 - - - +
249E ARG* 1.4 64.7 + - - +
251E ALA* 3.2 2.6 + - - +
252E ILE* 3.0 28.0 + - + +
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Residues in contact with ARG 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E TRP* 4.1 23.0 - - + -
156E VAL* 5.3 1.1 - - + +
176E SER 2.9 25.5 + - - -
177E ASN* 3.6 16.2 + - - +
178E ALA 3.3 23.0 + - - -
179E ILE* 3.7 31.6 - - + +
201E ASP* 3.5 17.4 + - - -
245E ALA 2.8 18.6 + - - +
246E SER 3.9 4.7 - - - +
248E ILE* 1.4 75.9 - - - +
250E ALA* 1.3 56.9 + - - +
252E ILE* 3.3 3.8 + - - +
253E GLU* 3.0 59.8 + - - +
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Residues in contact with ALA 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E SER 3.1 17.6 + - - +
247E ASN* 4.0 4.9 - - - +
248E ILE 3.3 0.4 - - - -
249E ARG* 1.3 74.3 - - - +
251E ALA* 1.3 57.2 + - - +
253E GLU* 3.0 3.2 + - - -
254E ASN* 2.7 47.7 + - - +
279E TYR* 3.7 25.6 - - + +
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E LEU* 3.9 15.7 - - + -
243E ARG* 4.6 2.2 - - - +
247E ASN 3.0 19.1 + - - +
248E ILE 3.2 4.5 + - - +
250E ALA* 1.3 76.3 - - - +
252E ILE* 1.3 59.7 + - - +
255E THR* 2.6 34.1 + - - -
276E ALA* 3.7 12.3 - - - +
279E TYR* 3.6 37.6 - - + -
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Residues in contact with ILE 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ILE* 4.4 17.0 - - + -
202E VAL* 4.4 16.0 - - + +
231E VAL* 4.1 27.8 - - + +
234E VAL* 4.3 11.4 - - + -
235E ALA* 3.8 32.3 - - + +
238E LEU* 3.8 11.4 - - + -
248E ILE* 3.0 24.6 + - + +
249E ARG* 3.6 7.0 - - - +
251E ALA* 1.3 78.8 - - - +
253E GLU* 1.4 66.8 + - + +
255E THR* 4.0 1.9 + - - -
256E ALA* 3.6 20.3 + - - +
271E VAL* 4.2 17.0 - - + +
272E ASN 5.5 0.2 + - - -
276E ALA* 4.6 3.4 - - - -
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Residues in contact with GLU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ILE* 4.1 5.3 - - + +
201E ASP* 3.4 20.3 - - + +
202E VAL* 5.1 2.9 - - + -
249E ARG* 3.0 61.3 + - + +
250E ALA* 3.9 2.2 - - - +
252E ILE* 1.4 85.8 - - + +
254E ASN* 1.3 71.9 + - - +
255E THR 3.5 1.0 + - - -
256E ALA* 3.7 8.8 + - - +
258E LYS* 4.2 3.8 + - - -
268E LYS* 3.3 53.1 + - + +
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Residues in contact with ASN 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ALA* 2.7 27.6 + - - +
253E GLU* 1.3 84.1 - - - +
255E THR* 1.3 63.5 + - - +
256E ALA 3.6 0.2 - - - -
258E LYS* 4.7 8.9 + - - +
268E LYS* 4.0 14.0 + - - -
279E TYR* 3.0 32.8 + - + +
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Residues in contact with THR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA 2.6 23.2 + - - +
252E ILE 4.0 1.6 + - - -
253E GLU 3.4 0.2 - - - -
254E ASN* 1.3 83.1 - - - +
256E ALA* 1.3 65.0 + - - +
257E ASP 3.5 0.7 + - - -
271E VAL* 6.2 0.2 - - - +
272E ASN* 3.7 11.5 + - - +
275E LYS* 3.0 53.1 + - + +
276E ALA* 3.2 17.5 + - - +
279E TYR* 3.7 24.0 - - + -
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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