Contacts of the strand formed by residues 41 - 47 (chain X) in PDB entry 3TDD
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 THR 41 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X LEU* 2.9 42.8 + - + -
38X SER* 3.0 28.8 + - - +
39X PRO 4.1 0.2 + - - -
40X HIS* 1.3 83.5 + - - +
42X LEU* 1.3 61.6 + - - +
73X GLU* 4.4 1.4 + - - -
74X LEU 4.7 5.7 + - - -
76X PRO* 4.3 15.9 - - + +
79X VAL* 4.3 12.7 - - + +
101X ILE* 3.7 27.8 - - + -
102X GLY 3.5 5.2 - - - +
103X GLY* 4.3 4.5 - - - -
184X ILE* 3.7 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LEU* 3.7 19.8 - - + +
34X THR* 3.3 33.4 - - + +
35X ARG 3.4 20.9 - - - +
36X GLN* 3.9 11.2 - - + +
37X LEU* 4.9 0.2 - - - -
41X THR* 1.3 76.5 - - - +
43X MET* 1.3 58.3 + - - +
44X SER 4.3 0.2 - - - -
100X LEU 3.8 0.2 - - - +
101X ILE* 3.5 4.3 - - - +
102X GLY 2.7 38.6 + - - +
176X LYS* 3.7 34.1 - - + +
178X VAL* 3.8 20.6 - - + +
184X ILE* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34X THR* 3.2 4.6 + - - -
35X ARG* 2.9 37.4 + - + +
37X LEU* 3.9 22.9 - - + -
42X LEU* 1.3 76.6 - - - +
44X SER* 1.3 70.0 + - - +
45X PHE* 4.0 6.5 - - + -
55X PHE* 4.6 2.9 - - + -
56X ALA* 3.7 36.1 - - + +
59X ILE* 4.1 19.7 - - + -
83X VAL* 4.4 10.3 - - - -
99X VAL* 3.8 26.0 - - + -
100X LEU 3.3 10.1 - - - +
101X ILE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X ILE* 3.6 11.8 - - - +
4X LEU 5.1 0.6 + - - -
14X LEU* 4.0 17.3 - - - +
16X SER* 3.7 18.8 - - - -
33X LYS 3.2 12.8 - - - -
34X THR* 3.9 4.3 - - - -
43X MET* 1.3 74.8 - - - +
45X PHE* 1.3 63.6 + - - +
99X VAL* 3.2 7.5 - - - +
100X LEU* 2.9 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X ILE* 3.6 8.6 - - - +
31X ASP* 6.0 0.2 - - - -
32X ASP 4.7 1.8 - - - -
33X LYS* 3.1 47.0 + - + +
34X THR* 3.7 26.7 - - - -
35X ARG* 4.1 8.7 - - + -
43X MET* 4.0 8.5 - - + -
44X SER* 1.3 79.7 - - - +
46X ALA* 1.3 63.7 + - - +
52X THR* 3.8 39.3 - - + -
53X VAL* 4.2 13.5 - - + -
56X ALA* 3.3 30.5 - - + -
97X VAL* 3.8 13.9 - - + -
98X ASN 3.2 12.3 - - - +
99X VAL* 3.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1X MET* 3.9 21.8 - - + -
1X ASP* 3.9 20.2 - - + +
3X ILE* 3.6 21.5 - - + -
45X PHE* 1.3 78.2 - - - +
47X GLY* 1.3 57.9 + - - +
52X THR* 3.6 8.7 - - - -
97X VAL* 3.6 1.0 - - - -
98X ASN* 2.9 36.2 + - + +
127X HIS* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1X MET* 4.3 16.5 - - - +
1X ASP* 4.3 9.1 + - - +
46X ALA* 1.3 77.7 - - - +
48X GLU* 1.3 66.4 + - - +
49X ALA* 3.5 2.4 + - - -
52X THR* 3.4 7.3 + - - -
96X GLN 3.3 9.4 - - - -
97X VAL* 4.6 0.2 - - - -
98X ASN* 5.2 0.9 - - - -
----------------------------------------------------------
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