Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 3U1J
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 LEU 29 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TYR* 3.8 12.0 - - - -
24E ASN* 2.9 31.4 + - - +
27E ALA* 3.7 23.3 - - + +
28E GLY* 1.3 80.7 - - - +
30E CYS* 1.3 68.0 + - - +
31E GLN* 3.7 27.4 - - + +
52E MET* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TYR* 4.0 19.4 - - + -
22E PHE 3.1 4.7 - - - +
23E TYR* 3.8 9.2 - - - -
29E LEU* 1.3 81.3 - - - +
31E GLN* 1.3 65.0 + - - +
48E ALA* 4.8 5.4 - - + +
51E CYS* 2.0 61.5 - - + -
52E MET* 3.6 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TYR* 3.2 11.8 - - - -
22E PHE* 2.8 50.9 + - + -
24E ASN* 2.8 35.8 + - + +
27E ALA* 4.0 6.7 - - - +
29E LEU* 3.7 24.2 + - + +
30E CYS* 1.3 79.2 - - - +
32E THR* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.2 3.4 - - + -
31B PHE* 3.7 35.1 - - + -
19E ILE* 3.8 18.8 - - + -
20E ARG 3.2 8.3 - - - +
21E TYR* 3.7 28.7 - - + +
22E PHE* 3.4 9.9 - - - -
31E GLN* 1.3 76.8 - - - +
33E PHE* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E PRO* 3.5 20.2 - - + -
10E TYR 3.5 31.2 - - - -
11E THR* 4.5 2.7 - - - -
19E ILE* 3.5 7.4 - - - +
20E ARG* 2.9 55.7 + - + +
21E TYR 3.7 13.9 - - - -
22E PHE* 3.6 26.0 - + + -
32E THR* 1.3 75.1 - - - +
34E VAL* 1.3 86.8 + - - +
35E TYR* 4.0 4.0 - - + -
43E ASN 3.9 11.2 - - - -
44E ASN* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 3.5 37.0 - - + -
11E THR* 2.8 32.3 + - + +
17E ARG* 3.7 26.2 - - + +
18E ILE 3.8 3.6 - - - +
19E ILE* 4.0 18.4 - - + -
33E PHE* 1.3 82.5 - - - +
35E TYR* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 5.5 3.3 + - - -
10E TYR 3.8 7.2 - - - -
11E THR 3.5 8.3 - - - -
12E GLY* 5.5 0.2 - - - -
16E ALA 3.5 2.9 - - - +
18E ILE* 2.8 50.3 + - + +
20E ARG* 3.7 46.0 - - + -
33E PHE* 3.7 11.3 + - + -
34E VAL* 1.3 74.6 - - - +
36E GLY* 1.3 66.3 + - - +
37E GLY* 3.3 23.5 + - - -
38E CYS* 3.2 37.1 + - - -
39E ARG 3.5 0.5 + - - -
40E ALA* 3.2 38.6 + - + +
44E ASN* 3.5 10.5 - - - -
----------------------------------------------------------
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