Contacts of the strand formed by residues 3 - 12 (chain E) in PDB entry 5U07
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 PHE 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E THR* 1.3 94.1 - - - +
4E VAL* 1.3 65.9 + - - +
5E ASP* 3.4 2.1 + - - +
236E ASN* 5.5 3.6 - - + -
237E VAL 3.5 4.0 - - - +
238E ASN* 3.4 45.3 - - + -
288E VAL* 4.6 1.1 - - - -
289E ARG* 2.9 42.2 + - + +
290E PHE 3.9 7.6 - - - -
291E ASP 3.9 15.9 - - - -
292E ARG* 4.2 3.6 - - - -
293E PRO* 3.6 43.5 - - + -
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Residues in contact with VAL 4 (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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3E PHE* 1.3 71.5 - - - +
5E ASP* 1.3 65.0 + - - +
6E ILE* 4.3 2.2 + - + +
235E ALA 3.9 0.5 - - - +
236E ASN* 3.5 1.3 - - - -
237E VAL* 2.8 43.9 + - + +
239E LEU* 3.6 34.5 - - + -
256E VAL* 5.1 6.1 - - + -
260E LEU* 4.1 29.8 - - + -
286E ILE* 4.4 13.9 - - + -
287E ALA 3.6 8.7 - - - +
288E VAL* 4.2 15.9 - - + +
363E MET 6.5 0.2 - - - -
364E VAL* 5.4 6.1 - - + -
367E ALA* 4.6 3.6 - - + -
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Residues in contact with ASP 5 (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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3E PHE 4.5 0.9 - - - +
4E VAL* 1.3 75.9 - - - +
6E ILE* 1.3 60.0 + - - +
7E HIS* 3.4 18.9 + - - -
234E TYR* 3.6 6.5 - - + +
235E ALA 3.2 4.5 - - - +
236E ASN* 3.0 24.5 - - - +
285E HIS 3.9 1.0 - - - +
286E ILE* 3.5 1.2 - - - +
287E ALA* 2.6 47.1 + - - +
289E ARG* 3.4 21.1 - - - +
293E PRO* 4.6 3.1 - - + -
294E ILE* 3.5 21.2 + - - +
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Residues in contact with ILE 6 (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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4E VAL* 5.4 1.8 - - + +
5E ASP* 1.3 74.1 - - - +
7E HIS* 1.3 72.8 + - - +
233E ARG 4.5 0.2 - - - -
234E TYR* 3.3 5.9 - - - -
235E ALA* 2.9 50.8 + - + +
237E VAL* 6.3 1.1 - - + -
259E PHE* 5.3 2.5 - - + -
260E LEU* 4.4 27.8 - - + +
263E PHE* 3.7 34.7 - - + -
264E LEU* 4.0 19.1 - - + -
284E VAL* 4.1 3.1 - - + -
285E HIS 3.7 2.9 - - - -
286E ILE* 3.9 27.4 - - + +
360E ILE* 5.5 0.9 - - + -
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Residues in contact with HIS 7 (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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5E ASP* 3.4 22.5 + - - -
6E ILE* 1.3 81.4 - - - +
8E ALA* 1.3 65.9 + - - +
232E TYR* 2.8 30.6 + - + +
233E ARG 3.4 5.6 - - - -
234E TYR* 3.4 15.4 - + - -
283E LEU* 5.5 0.9 - - + -
284E VAL* 3.5 2.3 - - - -
285E HIS* 2.9 62.6 + + + +
287E ALA* 5.2 0.6 - - - +
294E ILE 3.2 23.7 + - - -
296E PHE* 3.6 27.7 - + - -
318E LEU* 4.6 7.4 - - + -
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Residues in contact with ALA 8 (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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7E HIS* 1.3 79.4 - - - +
9E ILE* 1.3 67.1 + - - +
10E GLN 4.1 0.2 - - - -
231E PHE 3.9 0.2 - - - +
232E TYR* 3.6 4.8 - - - -
233E ARG* 2.9 55.7 + - + +
263E PHE* 4.5 10.5 - - + -
264E LEU* 4.8 0.9 - - + -
281E PRO* 4.3 10.5 - - + -
283E LEU* 3.1 13.2 - - - +
284E VAL* 4.3 10.1 - - + -
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Residues in contact with ILE 9 (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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8E ALA* 1.3 72.5 - - - +
10E GLN* 1.3 55.6 + - - +
194E VAL* 4.7 4.0 - - + -
230E THR* 3.3 25.6 - - - +
231E PHE 3.5 2.2 - - - +
232E TYR* 3.5 37.0 - - + -
281E PRO* 3.3 3.2 - - - +
282E ASP* 2.5 40.6 + - + +
283E LEU* 2.9 27.5 + - + +
300E PHE* 4.0 17.9 - - + -
311E THR* 5.3 2.9 - - - +
314E ALA* 4.4 16.6 - - + +
315E CYS* 4.9 11.7 - - - -
318E LEU* 4.4 12.1 - - + -
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Residues in contact with GLN 10 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E ALA 4.1 0.4 - - - -
9E ILE* 1.3 76.1 - - - +
11E THR* 1.3 70.1 + - - +
12E LEU* 3.9 10.1 + - + +
43E TRP* 3.8 8.0 - - - -
230E THR* 4.3 0.2 - - - -
231E PHE* 2.9 38.6 + - + +
233E ARG* 2.5 47.1 + - - -
264E LEU 4.7 1.7 + - - +
266E THR 5.2 0.4 + - - -
267E VAL* 3.9 18.2 - - - +
279E THR* 2.6 34.7 + - + -
280E LEU 4.3 2.7 - - - +
281E PRO* 3.3 24.7 - - + +
282E ASP 4.1 1.6 - - - +
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Residues in contact with THR 11 (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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10E GLN* 1.3 73.6 - - - +
12E LEU* 1.3 72.6 + - - +
13E PRO* 4.2 1.1 - - - +
229E GLY 3.6 6.1 - - - -
230E THR* 3.7 24.7 - - - +
279E THR* 3.4 16.2 + - - +
282E ASP* 3.0 27.1 + - - +
311E THR* 4.7 2.5 - - - -
30I TYR* 4.2 4.1 + - - -
298I PRO* 3.3 26.5 - - + +
301I GLU* 3.8 29.6 + - + +
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Residues in contact with LEU 12 (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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10E GLN* 4.1 17.0 - - + +
11E THR* 1.3 85.1 - - - +
13E PRO* 1.3 64.4 - - - +
15E SER* 3.7 16.3 + - - +
17E ILE* 4.0 20.0 - - + -
38E VAL* 5.2 1.3 - - + -
43E TRP* 5.3 9.6 - - + -
228E ALA* 3.6 4.0 - - - +
229E GLY 2.8 35.6 + - - +
231E PHE* 3.3 35.4 - - + -
267E VAL* 5.0 6.7 - - + -
268E PRO* 6.0 0.4 - - + -
277E ALA* 3.1 30.5 - - + +
279E THR* 4.1 7.6 - - - -
30I TYR* 4.5 3.9 - - - -
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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