Contacts of the strand formed by residues 229 - 238 (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 GLY 229 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E THR* 3.6 2.4 - - - -
12E LEU* 2.8 38.8 + - - +
15E SER* 5.4 0.2 + - - -
193E THR* 4.2 11.2 - - - +
195E HIS* 3.2 17.5 - - - -
228E ALA* 1.3 76.6 - - - +
230E THR* 1.3 57.3 + - - -
231E PHE* 3.6 7.0 + - - -
30I TYR* 5.2 5.5 - - - -
31I GLY 6.3 0.4 - - - -
301I GLU* 5.6 3.1 - - - -
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Residues in contact with THR 230 (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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9E ILE* 3.3 25.5 - - - +
11E THR* 3.7 26.6 + - - +
193E THR* 4.5 0.2 - - - +
194E VAL* 3.1 30.5 + - + +
195E HIS* 3.2 25.5 - - + +
229E GLY* 1.3 68.9 - - - -
231E PHE* 1.3 64.3 + - - +
310E TYR* 3.6 25.4 - - + +
311E THR* 5.0 3.3 - - - -
314E ALA* 5.0 1.6 - - + +
301I GLU* 4.8 4.4 + - - +
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Residues in contact with PHE 231 (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 3.9 0.3 - - - +
9E ILE* 3.5 5.1 - - - +
10E GLN* 2.9 38.3 + - + +
12E LEU* 3.3 36.3 - - + -
15E SER* 4.6 11.4 - - - -
17E ILE* 5.1 0.7 - - + -
36E THR* 3.8 16.4 - - - -
37E ARG 5.0 0.4 - - - -
38E VAL* 3.4 31.9 - - + -
43E TRP* 5.6 4.9 - + - -
191E ALA* 4.3 17.9 - - + -
192E PHE 3.4 4.9 - - - +
193E THR* 3.1 38.6 - - + -
194E VAL* 4.9 0.2 - - - -
227E SER* 5.9 0.9 - - - -
228E ALA 5.6 0.9 - - - -
229E GLY* 4.2 10.8 - - - -
230E THR* 1.3 73.7 - - - +
232E TYR* 1.3 58.5 + - - +
233E ARG* 4.1 6.4 + - + +
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Residues in contact with TYR 232 (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* 2.8 32.1 + - + -
8E ALA 3.6 3.1 - - - -
9E ILE* 3.5 24.9 - - + -
189E ALA* 6.1 0.9 - - + -
190E HIS 4.6 0.6 - - - +
191E ALA* 3.1 24.8 - - - -
192E PHE* 2.9 35.0 + + + +
194E VAL* 4.4 5.6 - - + -
230E THR 3.7 1.6 + - - -
231E PHE* 1.3 72.3 - - - +
233E ARG* 1.3 74.9 + - - +
234E TYR* 3.8 18.1 - - + +
295E SER* 5.5 0.7 - - - -
296E PHE* 3.2 20.3 + - + +
297E ALA* 4.1 18.6 - - + -
300E PHE* 3.6 22.4 - + + -
318E LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 233 (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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6E ILE 4.5 0.2 - - - -
7E HIS* 3.4 4.2 - - - -
8E ALA* 2.9 44.5 + - + +
10E GLN* 2.5 47.5 + - - +
43E TRP* 3.0 34.0 - - - -
188E PHE* 5.1 3.9 - - + -
189E ALA 5.7 0.4 - - - -
191E ALA* 3.7 19.5 - - + +
231E PHE* 4.4 8.7 - - + +
232E TYR* 1.3 85.5 - - - +
234E TYR* 1.3 62.0 + - - +
263E PHE* 2.4 64.9 + - + -
264E LEU* 4.5 1.6 + - - +
281E PRO* 3.7 16.0 - - - +
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Residues in contact with TYR 234 (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* 3.6 14.6 - - + +
6E ILE 3.3 7.9 - - - -
7E HIS* 3.4 36.8 - + - -
188E PHE* 3.9 6.7 - - - -
189E ALA* 3.1 38.8 + - + +
232E TYR* 3.8 16.4 - - + +
233E ARG* 1.3 77.3 - - - +
235E ALA* 1.3 68.4 + - - +
236E ASN* 2.3 47.8 + - - -
263E PHE* 4.4 2.8 - - - -
293E PRO* 3.4 11.6 - - - +
294E ILE 3.6 9.9 + - - -
295E SER* 3.7 26.0 + - - -
276F ALA* 3.6 25.4 - - + -
278F MET* 5.0 1.7 - - + +
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Residues in contact with ALA 235 (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 3.9 0.2 - - - +
5E ASP* 3.2 5.0 - - - +
6E ILE* 2.9 42.6 + - + +
186E VAL* 5.1 0.2 - - + -
187E GLN 3.0 12.6 - - - +
188E PHE* 4.0 6.3 - - + -
234E TYR* 1.3 81.8 - - - +
236E ASN* 1.3 63.9 + - - +
237E VAL* 5.6 0.2 - - - -
259E PHE* 4.6 13.5 - - + -
263E PHE* 3.7 25.1 - - + -
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Residues in contact with ASN 236 (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* 5.5 3.8 - - + -
4E VAL 3.5 2.9 - - - +
5E ASP* 3.0 12.5 - - - +
186E VAL* 3.2 9.7 - - - +
187E GLN* 2.7 64.0 + - + +
234E TYR* 2.3 44.7 + - - -
235E ALA* 1.3 71.8 - - - +
237E VAL* 1.3 70.7 + - - +
238E ASN 4.2 0.7 - - - +
293E PRO* 3.2 24.0 - - + +
276F ALA* 4.2 1.0 - - - +
278F MET* 4.2 3.2 - - - +
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Residues in contact with VAL 237 (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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2E THR 3.4 0.7 - - - +
3E PHE* 3.5 2.9 - - - -
4E VAL* 2.8 42.8 + - + +
6E ILE* 6.3 1.1 - - + -
169E LEU* 5.1 0.9 - - + -
185E ALA 3.5 7.0 - - - +
186E VAL* 3.7 9.0 - - + -
235E ALA 5.6 0.2 - - - -
236E ASN* 1.3 81.7 - - - +
238E ASN* 1.3 59.1 + - - +
239E LEU* 3.1 16.0 + - + +
242E LEU* 3.8 29.2 - - + -
256E VAL* 4.0 13.9 - - + -
259E PHE* 3.6 33.0 - - + -
260E LEU* 4.4 9.2 - - + -
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Residues in contact with ASN 238 (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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2E THR* 3.6 5.1 + - - +
3E PHE* 3.4 38.3 - - + -
185E ALA* 3.1 16.5 + - - +
236E ASN* 4.2 1.4 - - - +
237E VAL* 1.3 68.9 - - - +
239E LEU* 1.3 63.5 + - - +
240E ASP* 2.5 29.4 + - - +
241E ARG* 3.4 32.5 + - + +
242E LEU* 3.0 22.2 + - - +
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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