Contacts of the strand formed by residues 3 - 12 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 1.3 97.2 - - - +
4G VAL* 1.3 65.3 + - - +
5G ASP* 3.4 2.4 + - - +
187G GLN* 6.1 3.6 - - - -
236G ASN* 5.3 4.9 - - + +
237G VAL 3.4 3.6 - - - +
238G ASN* 3.3 46.7 - - + -
288G VAL* 3.7 1.3 - - - -
289G ARG* 2.9 38.8 + - + +
290G PHE 4.0 6.7 - - - -
291G ASP 3.9 15.3 - - - -
292G ARG* 4.1 3.4 - - - -
293G PRO* 3.6 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 4 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR 3.9 0.2 - - - -
3G PHE* 1.3 71.2 - - - +
5G ASP* 1.3 61.9 + - - +
6G ILE* 5.2 2.3 - - + +
235G ALA 3.9 0.7 - - - +
236G ASN* 3.4 2.0 - - - -
237G VAL* 2.8 44.5 + - + +
239G LEU* 3.8 31.6 - - + -
256G VAL* 4.9 8.1 - - + -
260G LEU* 4.2 22.7 - - + -
286G ILE* 3.9 24.0 - - + -
287G ALA 3.7 4.9 - - - +
288G VAL* 4.3 17.5 - - + +
363G MET* 5.7 2.2 - - + +
364G VAL* 5.9 3.8 - - + -
367G ALA* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 5 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G PHE 3.9 5.6 - - - +
4G VAL* 1.3 74.6 - - - +
6G ILE* 1.3 59.8 + - - +
7G HIS* 3.5 19.0 + - - -
234G TYR* 3.5 7.0 - - + +
235G ALA 3.2 4.7 - - - +
236G ASN* 3.0 24.9 - - - +
285G HIS 3.9 1.4 - - - +
286G ILE* 3.6 2.9 - - - +
287G ALA* 2.6 61.4 + - - +
289G ARG* 4.3 6.6 + - - +
293G PRO* 4.3 6.2 - - + +
294G ILE* 3.5 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 5.4 2.0 - - + +
5G ASP* 1.3 76.2 - - - +
7G HIS* 1.3 72.6 + - - +
233G ARG 3.9 0.2 - - - +
234G TYR* 3.3 6.1 - - - -
235G ALA* 2.9 46.5 + - + +
237G VAL* 6.3 0.9 - - + -
259G PHE* 5.4 2.9 - - + -
260G LEU* 4.4 21.3 - - + -
263G PHE* 3.4 41.7 - - + -
264G LEU* 4.0 17.3 - - + -
284G VAL* 4.2 3.8 - - + -
285G HIS 3.7 2.9 - - - -
286G ILE* 4.0 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ASP* 3.5 21.7 + - - -
6G ILE* 1.3 80.8 - - - +
8G ALA* 1.3 66.2 + - - +
232G TYR* 3.0 26.8 + - + -
233G ARG 3.4 7.4 - - - +
234G TYR* 3.5 16.4 - + - -
283G LEU* 5.6 0.4 - - - -
284G VAL* 3.5 1.9 - - - -
285G HIS* 2.9 66.1 + + + +
287G ALA* 5.0 0.2 - - - +
294G ILE 3.4 23.2 + - - -
296G PHE* 3.5 28.7 - + - -
318G LEU* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G HIS* 1.3 78.5 - - - +
9G ILE* 1.3 66.0 + - - +
10G GLN 4.1 0.2 - - - -
232G TYR* 3.6 4.3 - - - -
233G ARG* 2.9 56.0 + - + +
263G PHE* 4.4 11.2 - - + -
264G LEU* 4.7 0.2 - - + -
281G PRO* 4.3 14.8 - - + -
283G LEU* 3.1 13.5 - - - +
284G VAL* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA* 1.3 72.1 - - - +
10G GLN* 1.3 57.9 + - - +
11G THR* 5.3 0.7 - - + +
194G VAL* 4.7 4.7 - - + -
230G THR* 4.7 15.0 - - - +
231G PHE 3.5 5.2 - - - +
232G TYR* 3.6 35.0 - - + -
281G PRO* 3.3 3.0 - - - +
282G ASP* 2.6 40.7 + - + +
283G LEU* 2.9 27.3 + - + +
300G PHE* 4.0 18.6 - - + -
311G THR* 5.6 4.0 - - - +
314G ALA* 4.6 18.8 - - + +
315G CYS* 5.0 10.8 - - - -
318G LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA 4.1 0.2 - - - -
9G ILE* 1.3 75.9 - - - +
11G THR* 1.3 69.8 + - - +
12G LEU* 3.9 11.2 + - + +
43G TRP* 3.6 10.8 - - - -
230G THR* 4.3 0.4 - - - -
231G PHE* 2.9 39.4 + - + +
233G ARG* 2.8 38.6 + - - -
264G LEU 4.8 1.6 + - - +
266G THR 5.2 0.4 + - - -
267G VAL* 3.9 17.0 - - - +
279G THR* 2.4 37.2 + - + -
280G LEU 4.2 2.5 - - - -
281G PRO* 3.4 23.8 - - + +
282G ASP 4.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 11 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 4.0 11.5 + - - -
298F PRO* 3.2 29.0 - - + +
301F GLU* 4.8 2.0 - - + -
9G ILE* 5.4 1.6 - - + -
10G GLN* 1.3 74.7 - - - +
12G LEU* 1.3 65.5 + - - +
13G PRO* 4.3 0.5 - - - +
229G GLY 3.5 7.2 - - - -
230G THR* 3.5 30.1 - - + +
279G THR* 3.2 23.2 - - - +
282G ASP* 3.1 26.2 + - - +
311G THR* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 4.4 4.5 - - - -
10G GLN* 4.1 16.2 - - + +
11G THR* 1.3 81.9 - - - +
13G PRO* 1.3 64.2 - - + +
15G SER* 3.6 15.5 - - - +
17G ILE* 3.8 21.3 - - + -
38G VAL* 5.2 1.1 - - + -
43G TRP* 5.3 9.6 - - + -
228G ALA* 3.4 4.5 - - - +
229G GLY 2.9 35.9 + - - +
231G PHE* 3.3 34.1 - - + -
267G VAL* 5.1 5.4 - - + -
277G ALA* 3.2 32.1 - - + +
279G THR* 4.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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