Contacts of the strand formed by residues 33 - 38 (chain G) in PDB entry 5U0A
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 LYS 33 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 4.2 1.3 - - - -
30G TYR 2.9 28.4 + - - +
31G GLY 3.2 4.0 - - - +
32G GLY* 1.3 80.2 - - - +
34G GLU* 1.3 69.2 + - - +
35G ARG* 3.3 5.1 - - - +
196G GLY* 3.5 30.1 - - - -
303G ALA* 3.8 28.2 + - + +
304G LEU 4.7 7.5 + - - -
305G TYR* 5.3 10.5 + - - +
307H SER* 3.7 27.5 + - - +
308H ASP* 5.3 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G THR* 3.2 40.4 + - + +
28G VAL 3.4 7.4 - - - +
29G VAL* 4.1 15.6 - - + +
32G GLY 4.4 0.4 + - - -
33G LYS* 1.3 73.6 - - - +
35G ARG* 1.3 62.1 + - - +
196G GLY* 3.3 8.0 - - - -
197G THR 3.1 34.1 + - - +
198G THR* 5.4 3.3 - - - -
199G VAL* 4.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G THR* 4.2 2.5 - - - -
28G VAL* 2.7 40.6 + - + +
30G TYR* 3.1 41.7 + - - -
31G GLY* 4.3 1.6 + - - -
33G LYS* 3.3 6.9 + - - +
34G GLU* 1.3 81.1 - - - +
36G THR* 1.3 63.2 + - - +
37G ARG 3.5 0.2 + - - -
192G PHE* 4.0 7.5 - - + +
193G THR* 3.0 37.3 + - - +
194G VAL 3.6 8.2 + - - -
195G HIS 3.9 6.3 - - - +
196G GLY* 4.2 1.6 - - - -
197G THR* 3.9 2.0 - - - +
300G PHE 2.2 27.5 + - - -
301G GLU 2.4 29.4 + - - -
303G ALA* 3.0 34.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PRO* 3.7 18.5 - - - +
26G LYS 3.3 11.2 + - - -
27G THR* 4.0 11.9 - - - +
35G ARG* 1.3 71.8 - - - +
37G ARG* 1.3 63.2 + - - +
192G PHE* 3.5 0.9 - - - -
193G THR* 3.1 42.9 + - + +
197G THR* 3.0 21.9 + - + +
199G VAL* 6.5 0.4 - - - -
227G SER* 3.5 23.9 + - - +
228G ALA 4.9 0.9 - - - +
231G PHE* 3.8 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ASN 4.7 4.2 - - - +
25G PRO* 5.5 0.3 - - - +
26G LYS* 2.5 65.2 + - - +
27G THR 3.9 8.7 + - - +
28G VAL* 3.3 28.1 - - + +
36G THR* 1.3 79.7 + - - +
38G VAL* 1.3 64.6 + - - +
39G SER* 3.7 5.5 + - - -
190G HIS* 3.6 30.6 + - + -
191G ALA 3.1 13.9 - - - +
192G PHE* 4.1 4.7 - - + -
231G PHE* 5.2 0.4 - - - -
14H TYR* 2.7 38.9 + - - -
201H VAL 4.3 4.2 + - - -
202H ASP* 2.7 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ILE* 3.4 20.6 - - + -
18G ASN* 4.0 12.3 - - + +
37G ARG* 1.3 73.7 - - - +
39G SER* 1.3 66.1 + - - +
42G SER* 3.4 22.2 - - - +
43G TRP* 3.7 27.1 - - + -
190G HIS* 3.8 2.5 - - - -
191G ALA* 2.7 33.1 + - + +
231G PHE* 3.4 33.0 - - + -
268G PRO* 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