Contacts of the strand formed by residues 3 - 12 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F THR* 1.3 89.0 - - - +
4F VAL* 1.3 64.4 + - - +
5F ASP* 3.4 3.8 + - - +
187F GLN* 6.0 4.7 - - - -
236F ASN* 5.3 4.3 - - + +
237F VAL 3.5 4.0 - - - +
238F ASN* 3.3 45.8 - - + -
288F VAL* 4.6 1.1 - - - -
289F ARG* 2.9 37.8 + - + +
290F PHE 4.1 4.3 - - - -
291F ASP 3.7 17.3 - - - -
292F ARG* 3.9 6.3 - - - -
293F PRO* 3.5 48.0 - - + -
278G MET* 6.3 1.1 - - + -
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Residues in contact with VAL 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F PHE* 1.3 73.1 - - - +
5F ASP* 1.3 61.6 + - - +
6F ILE* 4.3 1.7 + - + +
235F ALA 3.9 0.5 - - - +
236F ASN* 3.5 1.4 - - - -
237F VAL* 2.8 43.8 + - + +
239F LEU* 3.6 34.3 - - + -
256F VAL* 4.9 7.4 - - + -
260F LEU* 4.0 22.9 - - + -
286F ILE* 4.0 23.6 - - + -
287F ALA 3.7 4.5 - - - +
288F VAL* 4.2 18.2 - - + +
363F MET* 5.9 1.3 - - + -
364F VAL* 5.7 5.4 - - + -
367F ALA* 4.6 3.6 - - + -
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Residues in contact with ASP 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F PHE 3.8 2.3 - - - +
4F VAL* 1.3 74.0 - - - +
6F ILE* 1.3 60.4 + - - +
7F HIS* 3.6 11.2 + - - -
234F TYR* 3.7 5.8 - - + +
235F ALA 3.2 4.9 - - - +
236F ASN* 3.0 25.1 - - - +
285F HIS 3.8 1.6 - - - +
286F ILE* 3.6 3.4 - - - +
287F ALA* 2.6 48.0 + - - +
289F ARG* 3.7 18.2 - - - +
293F PRO* 4.6 3.8 - - + -
294F ILE 3.5 30.1 + - - +
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Residues in contact with ILE 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 5.4 1.8 - - + +
5F ASP* 1.3 73.6 - - - +
7F HIS* 1.3 72.4 + - - +
233F ARG 4.6 0.2 - - - -
234F TYR* 3.4 6.0 - - - -
235F ALA* 2.9 51.5 + - + +
237F VAL* 6.2 1.1 - - + -
259F PHE* 5.4 1.8 - - + -
260F LEU* 4.3 23.3 - - + -
263F PHE* 3.6 34.3 - - + -
264F LEU* 4.0 17.5 - - + -
284F VAL* 4.2 4.0 - - + -
285F HIS 3.7 3.1 - - - -
286F ILE* 4.0 32.1 - - + +
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Residues in contact with HIS 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ASP* 3.6 21.1 + - - -
6F ILE* 1.3 80.7 - - - +
8F ALA* 1.3 65.4 + - - +
232F TYR* 3.0 26.8 + - + -
233F ARG 3.4 7.2 - - - +
234F TYR* 3.4 16.0 - + - -
283F LEU* 5.4 0.9 - - - -
284F VAL* 3.5 2.3 - - - -
285F HIS* 2.9 65.4 + + + +
287F ALA* 5.3 0.4 - - - +
294F ILE 3.3 23.4 + - - -
296F PHE* 3.5 30.3 - + - -
318F LEU* 4.7 8.5 - - + -
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Residues in contact with ALA 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F HIS* 1.3 78.1 - - - +
9F ILE* 1.3 69.7 + - - +
231F PHE 4.0 0.2 - - - +
232F TYR* 3.9 1.3 - - - -
233F ARG* 2.9 51.4 + - + +
263F PHE* 4.4 15.0 - - + -
264F LEU* 4.5 2.2 - - + -
281F PRO* 4.2 15.5 - - + -
283F LEU* 3.0 13.0 - - - +
284F VAL* 4.4 5.6 - - + -
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Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ALA* 1.3 72.3 - - - +
10F GLN* 1.3 58.5 + - - +
11F THR* 5.3 1.1 - - + +
194F VAL* 4.7 4.7 - - + -
230F THR* 4.8 13.0 - - - -
231F PHE 3.6 6.5 - - - +
232F TYR* 3.6 39.0 - - + -
281F PRO* 3.3 2.5 - - - +
282F ASP* 2.6 42.2 + - + +
283F LEU* 2.9 25.2 + - + +
300F PHE* 4.2 11.0 - - + -
311F THR* 5.6 3.8 - - - +
314F ALA* 4.5 18.4 - - + +
315F CYS* 5.1 10.5 - - - -
318F LEU* 4.1 19.7 - - + -
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Residues in contact with GLN 10 (chain F).
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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8F ALA 4.1 0.2 - - - -
9F ILE* 1.3 75.6 - - - +
11F THR* 1.3 69.4 + - - +
12F LEU* 4.0 10.0 + - + +
43F TRP* 3.7 8.1 - - - -
230F THR* 4.4 0.2 - - - -
231F PHE* 2.9 39.2 + - + +
233F ARG* 2.4 47.1 + - - +
264F LEU 4.7 0.9 + - - +
266F THR 5.0 0.6 + - - -
267F VAL* 3.9 18.8 - - - +
279F THR* 2.5 35.0 + - + -
280F LEU 4.3 2.7 - - - -
281F PRO* 3.3 24.1 - - + +
282F ASP 4.2 2.0 - - - +
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Residues in contact with THR 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 3.8 11.8 + - - -
298E PRO* 3.2 27.2 - - + +
301E GLU* 4.8 3.4 - - + -
9F ILE* 5.4 2.0 - - + -
10F GLN* 1.3 77.7 - - - +
12F LEU* 1.3 64.1 + - - +
13F PRO* 4.3 0.2 - - - +
229F GLY 3.5 6.7 - - - -
230F THR* 3.5 31.6 - - + +
279F THR* 3.4 23.5 + - - +
282F ASP* 3.2 25.3 + - - +
311F THR* 3.7 12.3 - - + -
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 4.3 3.2 - - - -
10F GLN* 4.2 14.6 - - + +
11F THR* 1.3 82.3 - - - +
13F PRO* 1.3 64.6 - - - +
15F SER* 3.7 18.8 - - - +
17F ILE* 3.7 23.6 - - + -
43F TRP* 5.2 8.3 - - + -
228F ALA* 3.5 4.0 - - - +
229F GLY 2.8 35.0 + - - +
231F PHE* 3.4 35.0 - - + -
267F VAL* 4.9 6.7 - - + -
277F ALA* 3.2 30.1 - - + +
279F THR* 4.2 9.0 - - - +
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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