Contacts of the helix formed by residues 302 - 314 (chain E) in PDB entry 4U8T
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 PRO 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C GLU* 3.5 33.9 - - + +
244C ASN* 5.4 2.7 - - - +
284E ILE* 4.4 14.6 - - + -
285E PRO* 4.4 19.5 - - + -
286E ALA* 5.8 4.0 - - + +
300E GLU 4.2 4.5 - - - +
301E ILE* 1.3 94.5 - - + +
303E ALA* 1.3 57.8 + - - +
304E THR* 4.9 1.8 - - - +
305E ILE* 3.1 19.0 - - + +
306E SER* 2.7 34.5 + - - -
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Residues in contact with ALA 303 (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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215C GLU* 3.3 12.7 + - - +
178E SER 4.9 5.2 - - - +
180E PHE* 3.9 22.2 - - + -
301E ILE 3.9 0.4 + - - -
302E PRO* 1.3 70.4 - - - +
304E THR* 1.3 69.2 + - + +
306E SER* 3.0 3.3 + - - -
307E LYS* 2.9 42.3 + - - +
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Residues in contact with THR 304 (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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215C GLU* 4.8 4.0 + - - +
302E PRO* 3.6 1.4 - - - +
303E ALA* 1.3 77.8 - - + +
305E ILE* 1.3 73.7 + - - +
307E LYS* 3.2 16.0 + - + +
308E SER* 3.0 25.2 + - - -
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Residues in contact with ILE 305 (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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282E PHE* 3.6 37.7 - - + -
283E LEU 3.9 12.1 - - - +
284E ILE* 3.6 26.2 - - + -
285E PRO* 5.5 1.6 - - + -
301E ILE* 3.9 9.2 - - + -
302E PRO* 3.1 46.0 - - + +
304E THR* 1.3 79.8 + - - +
306E SER* 1.3 55.1 + - - +
308E SER* 3.2 9.1 + - - -
309E ILE* 2.9 30.5 + - + +
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Residues in contact with SER 306 (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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180E PHE* 3.3 46.7 - - - +
226E LEU* 5.8 4.6 - - - +
301E ILE* 3.5 13.7 - - - +
302E PRO 2.7 19.0 + - - -
303E ALA 3.0 9.7 + - - -
305E ILE* 1.3 76.3 - - - +
307E LYS* 1.3 53.4 + - - +
309E ILE* 3.0 8.9 + - - +
310E LEU* 2.7 40.2 + - - +
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Residues in contact with LYS 307 (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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174E VAL* 4.5 31.1 + - + -
176E ASP* 5.1 9.7 + - - +
180E PHE* 4.9 9.0 - - + -
303E ALA* 2.9 33.8 + - - +
304E THR* 3.6 14.9 - - + +
306E SER* 1.3 75.1 - - - +
308E SER* 1.3 61.9 + - - +
310E LEU* 3.4 9.1 + - - +
311E LYS* 3.2 26.8 + - - +
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Residues in contact with SER 308 (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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282E PHE* 3.8 22.8 - - - -
304E THR 3.0 13.4 + - - -
305E ILE* 3.4 11.5 - - - -
307E LYS* 1.3 78.2 - - - +
309E ILE* 1.3 60.6 + - - +
311E LYS* 3.3 33.8 + - - +
312E LEU* 3.2 20.6 - - - +
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Residues in contact with ILE 309 (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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226E LEU* 4.1 21.1 - - + -
235E PHE* 6.3 0.7 - - + -
279E LEU* 3.7 18.8 - - + -
282E PHE* 3.8 20.6 - - + -
292E VAL* 4.1 34.3 - - + -
301E ILE* 4.6 5.4 - - + -
305E ILE* 2.9 30.5 + - + +
306E SER* 3.0 8.3 + - - +
308E SER* 1.3 72.0 - - - +
310E LEU* 1.3 68.1 + - + +
312E LEU* 3.1 24.0 + - - +
313E PHE* 3.5 25.1 + - + -
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Residues in contact with LEU 310 (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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172E ILE* 4.6 23.1 - - + -
174E VAL* 4.0 26.9 - - + -
180E PHE* 4.5 16.4 - - + -
224E TYR* 5.0 8.1 - - + -
226E LEU* 4.2 12.8 - - + -
238E VAL* 3.8 34.3 - - + -
306E SER* 2.7 22.5 + - - +
307E LYS* 3.7 9.4 - - - +
308E SER 3.3 0.4 - - - -
309E ILE* 1.3 72.4 - - + +
311E LYS* 1.3 62.4 + - - +
313E PHE* 2.9 21.9 + - + +
314E LYS* 3.2 19.4 + - + +
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Residues in contact with LYS 311 (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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307E LYS 3.2 13.7 + - - +
308E SER* 3.4 36.3 + - - +
309E ILE 3.2 0.6 - - - -
310E LEU* 1.3 76.8 - - - +
312E LEU* 1.3 61.1 + - + +
314E LYS* 2.9 42.0 + - - +
315E TYR* 3.5 19.3 - - + -
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Residues in contact with LEU 312 (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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272E ARG* 3.3 24.6 + - - -
274E VAL* 3.8 17.1 - - + +
278E SER* 3.3 43.5 - - - +
279E LEU* 3.9 14.8 - - + -
281E GLN* 5.0 2.7 - - - +
282E PHE* 4.4 11.7 - - + -
308E SER 3.2 26.9 - - - +
309E ILE* 3.1 11.6 + - - +
311E LYS* 1.3 82.2 - - + +
313E PHE* 1.3 60.8 + - + +
315E TYR* 4.5 15.3 + - + +
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Residues in contact with PHE 313 (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* 3.8 9.7 - - - +
172E ILE* 5.7 0.2 - - + -
226E LEU* 4.5 7.6 - - + -
235E PHE* 3.9 27.6 - + + -
236E CYS 4.4 0.2 - - - -
237E GLY* 3.8 19.1 - - - -
238E VAL* 3.8 21.8 - - + -
270E VAL* 3.8 35.5 - - + +
272E ARG* 3.0 45.5 + - - +
274E VAL* 3.8 21.1 - - + -
279E LEU* 5.6 0.9 - - + -
309E ILE* 3.5 35.6 + - + -
310E LEU* 2.9 17.5 + - + +
312E LEU* 1.3 78.6 - - + +
314E LYS* 1.3 57.0 + - + +
315E TYR 3.5 0.3 + - - -
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Residues in contact with LYS 314 (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* 4.2 8.7 - - - -
169E PRO* 5.2 10.1 - - + +
170E PRO 5.3 8.1 - - - +
171E TRP* 5.3 1.1 - - - +
172E ILE* 3.7 51.7 + - + +
270E VAL* 5.7 0.7 - - + -
310E LEU* 3.3 21.2 - - + +
311E LYS* 2.9 27.0 + - - +
313E PHE* 1.3 76.7 - - - +
315E TYR* 1.3 67.2 + - - +
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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