Contacts of the helix formed by residues 265 - 274 (chain E) in PDB entry 3TMP
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 ASP 265 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A THR 4.8 5.9 - - - +
46B ALA 5.1 0.3 - - - +
47B GLY* 4.1 18.0 - - - +
48B LYS* 5.7 1.4 - - - +
264E GLU* 1.3 72.1 - - - +
266E PHE* 1.3 68.6 + - - +
267E THR* 3.5 10.8 + - - -
268E THR* 2.6 41.3 + - - +
269E TYR* 3.0 18.5 + - - +
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Residues in contact with PHE 266 (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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46B ALA* 3.9 13.9 + - + +
47B GLY* 5.8 0.8 - - - -
251E LEU* 3.5 33.4 - - + -
252E MET* 4.0 9.0 - - - -
255E ALA* 3.8 18.8 - - + -
258E PHE* 3.9 14.8 - - + -
259E SER* 3.6 42.0 - - - -
262E VAL* 3.9 27.8 - - + -
264E GLU 3.1 4.1 + - - -
265E ASP* 1.3 75.4 + - - +
267E THR* 1.3 62.6 + - - +
269E TYR* 3.2 9.8 + + - +
270E ILE* 3.0 54.2 + - + +
283E ILE* 5.7 0.2 - - + -
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Residues in contact with THR 267 (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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45B PHE 4.3 0.9 + - - -
46B ALA* 3.4 16.6 + - - +
48B LYS* 4.0 38.2 - - + +
252E MET* 4.1 20.7 - - + +
265E ASP* 3.4 10.1 + - - -
266E PHE* 1.3 77.4 - - - +
268E THR* 1.3 57.2 + - - +
270E ILE* 3.4 5.6 + - + +
271E ASN* 2.9 46.5 + - - +
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Residues in contact with THR 268 (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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264E GLU* 3.9 13.3 - - - +
265E ASP* 2.6 35.8 + - - +
267E THR* 1.3 72.4 - - - +
269E TYR* 1.3 67.0 + - - +
271E ASN* 3.4 10.3 + - + +
272E ARG* 3.2 23.2 + - + +
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Residues in contact with TYR 269 (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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176E ASN* 3.8 12.7 + - + -
177E SEP 3.7 21.4 + - - -
251E LEU* 4.8 0.2 - - + -
262E VAL* 3.7 29.6 - - + -
264E GLU* 3.4 36.5 + - + -
265E ASP 3.0 7.8 + - - +
266E PHE* 3.4 12.3 - + - +
268E THR* 1.3 77.6 - - - +
270E ILE* 1.3 78.7 + - + +
272E ARG* 3.3 7.5 + - - +
273E LYS* 3.0 53.5 + - + +
281E ASN* 5.0 1.2 - - - +
283E ILE* 3.6 21.3 - - + +
284E GLU* 2.3 38.7 + - - -
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Residues in contact with ILE 270 (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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248E MET* 3.9 15.9 - - + +
251E LEU* 3.7 37.9 - - + -
252E MET* 3.7 33.9 - - + -
266E PHE* 3.0 26.0 + - + +
267E THR 3.9 3.1 - - - +
269E TYR* 1.3 90.3 - - + +
271E ASN* 1.3 68.9 + - - +
273E LYS* 3.0 3.1 + - - +
274E ARG* 2.9 45.0 + - - +
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Residues in contact with ASN 271 (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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48B LYS* 5.8 1.0 - - - +
267E THR* 2.9 41.1 + - - +
268E THR* 3.7 9.4 - - + +
269E TYR 3.4 0.2 - - - -
270E ILE* 1.3 79.0 - - - +
272E ARG* 1.3 60.9 + - - +
274E ARG* 3.6 22.3 + - - +
275E LYS* 4.0 9.7 + - - +
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Residues in contact with ARG 272 (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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175E TYR* 3.3 48.5 - - - +
177E SEP 2.9 43.2 + - - -
181E TYR* 3.6 8.5 + - - -
264E GLU* 2.8 29.1 + - - -
268E THR* 3.2 10.1 + - + +
269E TYR* 3.6 17.3 + - - +
270E ILE 3.2 0.4 - - - -
271E ASN* 1.3 77.3 - - - +
273E LYS* 1.3 62.7 + - - +
275E LYS* 3.1 34.1 + - + +
278E CYS* 3.3 32.9 - - + +
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Residues in contact with LYS 273 (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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177E SEP 2.7 38.7 + - - -
244E ARG* 2.8 31.6 + - - +
248E MET* 3.5 27.1 - - + +
269E TYR* 3.0 46.6 + - + +
270E ILE* 3.0 4.6 + - - +
272E ARG* 1.3 78.3 - - - +
274E ARG* 1.3 59.1 + - - +
275E LYS 3.2 0.2 - - - -
278E CYS* 3.5 17.7 - - + +
279E HIS 3.0 23.0 + - - +
280E GLY* 5.2 0.4 - - - -
281E ASN* 3.7 2.6 - - - +
284E GLU* 3.0 33.2 + - + +
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Residues in contact with ARG 274 (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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60B ASN* 3.7 20.0 - - - +
244E ARG* 3.4 12.5 - - - +
245E LYS* 3.9 18.7 + - - +
248E MET* 3.6 43.2 + - + +
249E ASP* 2.8 31.8 + - - +
252E MET* 4.0 13.9 - - - +
270E ILE* 2.9 25.5 + - - +
271E ASN* 3.8 16.2 + - - +
272E ARG 3.2 0.6 - - - -
273E LYS* 1.3 75.7 - - - +
275E LYS* 1.3 63.3 + - - +
276E ASN* 3.5 1.9 + - - +
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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