Contacts of the helix formed by residues 259 - 274 (chain E) in PDB entry 3T2I
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 GLY 259 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E SER* 2.7 26.0 + - - -
246E GLN* 4.8 2.2 - - - -
257E GLY 3.6 0.4 - - - -
258E ILE* 1.3 83.8 - - - +
260E ARG* 1.3 63.4 + - - -
261E ASP 3.5 2.4 + - - -
262E LYS 3.7 0.2 + - - -
263E LEU* 3.2 20.8 + - - +
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Residues in contact with ARG 260 (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 LEU* 3.8 21.2 - - + +
178E PHE* 3.4 59.8 - - - +
186E TRP* 3.7 14.6 - - + -
245E SER* 3.2 17.3 - - - +
246E GLN* 4.1 13.9 + - - +
259E GLY* 1.3 69.7 - - - -
261E ASP* 1.3 73.9 + - - +
263E LEU* 3.2 7.5 + - - +
264E GLY* 2.9 21.3 + - - -
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Residues in contact with ASP 261 (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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87E VAL* 5.7 11.4 - - + +
259E GLY 3.5 0.4 - - - -
260E ARG* 1.3 83.4 + - - +
262E LYS* 1.3 59.9 + - + +
264E GLY* 3.2 4.0 + - - -
265E LYS* 2.9 35.1 + - + +
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Residues in contact with LYS 262 (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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258E ILE* 3.7 36.7 + - + +
259E GLY 3.7 1.4 + - - -
260E ARG 3.3 0.2 - - - -
261E ASP* 1.3 76.3 - - + +
263E LEU* 1.3 66.5 + - - +
265E LYS* 3.8 1.1 - - + +
266E ILE* 3.0 30.0 + - - +
296E TYR* 3.2 35.3 - - + +
302E GLU* 2.8 34.7 + - + +
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Residues in contact with LEU 263 (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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171E ILE* 4.3 15.3 - - + -
175E LEU* 4.3 12.6 - - + -
186E TRP* 3.8 28.3 - - + -
241E ALA* 3.6 43.3 - - + +
244E ILE* 4.0 17.5 - - + -
245E SER* 4.1 6.1 - - - -
258E ILE* 4.5 1.4 - - - +
259E GLY 3.2 14.9 + - - +
260E ARG 3.2 7.7 + - - +
262E LYS* 1.3 74.9 - - - +
264E GLY* 1.3 58.1 + - - +
266E ILE* 3.7 2.1 - - - +
267E PHE* 2.9 53.4 + - + +
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Residues in contact with GLY 264 (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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83E TYR* 4.6 1.1 - - - -
88E HIS* 3.7 10.8 - - - -
172E PHE* 3.8 7.8 - - - -
175E LEU* 3.7 23.1 - - - +
260E ARG 2.9 11.8 + - - -
261E ASP* 3.6 4.0 - - - -
263E LEU* 1.3 77.8 - - - +
265E LYS* 1.3 57.3 + - - +
267E PHE* 5.0 0.2 - - - -
268E TYR* 2.8 35.2 + - - +
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Residues in contact with LYS 265 (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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87E VAL* 4.0 21.7 + - + +
88E HIS* 4.4 21.1 + - + +
89E ASN* 5.8 3.6 - - - +
261E ASP* 2.9 23.4 + - + +
262E LYS* 3.2 1.8 + - + +
264E GLY* 1.3 75.6 - - - +
266E ILE* 1.3 62.9 + - - +
268E TYR* 4.0 2.3 - - - +
269E ARG* 3.1 26.2 + - - +
295E LEU* 3.8 23.9 - - + +
296E TYR* 3.7 24.2 - - - +
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Residues in contact with ILE 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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244E ILE* 4.9 3.1 - - + -
258E ILE* 3.8 25.8 - - + -
262E LYS 3.0 18.4 + - - +
263E LEU* 3.7 3.8 - - - +
265E LYS* 1.3 79.5 - - - +
267E PHE* 1.3 66.1 + - + +
269E ARG 3.5 0.2 + - - -
270E ALA* 3.0 26.7 + - - +
288E ALA* 3.6 36.8 - - + +
291E SER* 3.5 6.3 - - - -
292E ALA* 3.8 24.5 - - + -
295E LEU* 4.2 6.7 - - + -
296E TYR* 3.9 20.9 - - + -
302E GLU* 4.6 0.9 - - + -
306E VAL* 3.9 14.1 - - + -
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Residues in contact with PHE 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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168E ILE* 3.9 20.6 - - + +
171E ILE* 3.7 34.3 - - + -
172E PHE* 3.9 17.7 - - + -
237E ILE* 4.2 5.6 - - + -
241E ALA* 4.5 6.5 - - + -
244E ILE* 3.8 26.7 - - + -
263E LEU* 2.9 34.1 + - + +
266E ILE* 1.3 82.1 - - + +
268E TYR* 1.3 61.2 + - - +
270E ALA* 3.4 5.4 + - + +
271E LEU* 2.9 29.5 + - - +
284E LEU* 4.2 27.4 - - + -
288E ALA* 4.6 10.3 - - + -
310E PHE* 4.1 21.3 - + - -
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Residues in contact with TYR 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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84E TYR* 4.1 22.4 - + - -
88E HIS* 3.6 52.1 + + + +
90E ARG* 3.0 42.0 + - - +
148E VAL* 4.6 4.9 - - + -
172E PHE* 3.4 11.7 - + + -
264E GLY 2.8 19.7 + - - +
265E LYS* 4.0 2.7 - - - +
267E PHE* 1.3 77.2 - - - +
269E ARG* 1.3 58.0 + - - +
271E LEU* 3.3 7.3 + - + +
272E THR* 2.8 59.4 + - + +
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Residues in contact with ARG 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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265E LYS 3.1 19.2 + - - +
268E TYR* 1.3 76.6 - - + +
270E ALA* 1.3 59.9 + - - +
272E THR* 3.8 5.8 - - - -
273E GLN* 2.8 56.2 + - + +
274E TYR* 4.3 3.4 + - + -
291E SER* 3.5 31.0 - - - +
294E ASP* 2.8 39.3 + - - +
295E LEU* 4.0 21.4 - - + +
2003E SAR 3.0 37.9 + - - -
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Residues in contact with ALA 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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168E ILE* 6.3 0.2 - - + -
266E ILE 3.0 18.0 + - - +
267E PHE* 3.7 8.1 - - + +
269E ARG* 1.3 75.5 - - - +
271E LEU* 1.3 56.6 + - - +
274E TYR* 2.9 13.8 + - - -
275E LEU* 2.9 34.3 + - + -
284E LEU* 4.7 9.2 - - + -
287E ALA* 4.0 24.0 - - + +
288E ALA* 4.3 5.6 - - + +
291E SER* 3.1 13.4 + - - +
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Residues in contact with LEU 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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145E THR* 5.3 0.7 - - + -
148E VAL* 4.0 20.0 - - + -
149E THR* 3.9 18.2 - - + +
152E THR* 3.5 20.9 - - - +
153E ALA* 3.4 39.4 + - + +
155E LEU* 4.3 7.2 - - + -
168E ILE* 3.8 30.3 - - + -
172E PHE* 4.8 9.2 - - + -
267E PHE 2.9 17.7 + - - +
268E TYR* 3.6 9.2 - - + +
269E ARG 3.3 0.2 - - - -
270E ALA* 1.3 78.7 - - - +
272E THR* 1.3 62.8 + - + +
275E LEU* 4.0 19.3 + - + +
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Residues in contact with THR 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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90E ARG* 4.3 1.8 - - - +
152E THR* 3.7 32.7 - - + -
268E TYR* 2.8 59.1 + - + +
269E ARG* 3.7 7.3 + - - -
271E LEU* 1.3 80.0 - - + +
273E GLN* 1.3 77.0 + - - +
275E LEU 5.9 0.2 - - - -
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Residues in contact with GLN 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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269E ARG* 2.8 38.1 + - + +
272E THR* 1.3 103.7 + - - +
274E TYR* 1.3 84.0 + - + +
275E LEU 5.2 1.6 - - - -
2003E SAR 4.3 16.4 - - - +
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Residues in contact with TYR 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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269E ARG* 4.0 7.5 + - - -
270E ALA 2.9 4.5 + - - +
272E THR 3.9 0.2 - - - -
273E GLN* 1.3 103.7 - - + +
275E LEU* 1.3 67.1 - - - +
276E THR* 3.7 11.4 + - - +
279E SER* 4.6 0.9 + - - -
287E ALA* 3.7 28.7 - - + +
290E GLN* 3.3 27.3 + - + +
291E SER* 3.4 24.9 - - - -
294E ASP* 2.4 36.1 + - - -
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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
------------------------------------------------------------
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