Contacts of the strand formed by residues 55 - 59 (chain A) in PDB entry 5DPT
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 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 4.1 25.8 + - + -
16A HIS* 6.2 0.2 - - + -
24A GLU* 4.3 14.8 + - - -
38A VAL 3.9 2.7 - - - -
39A ILE* 4.0 21.8 - - + -
53A LYS* 4.8 5.3 - - - +
54A ARG* 1.3 86.8 + - + +
56A TYR* 1.3 66.8 + - - +
111A PHE* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL 3.4 1.7 - - - +
37A PRO* 3.4 3.5 - - - +
38A VAL* 2.7 40.7 + - + +
39A ILE* 5.4 0.2 - - - +
40A VAL* 3.8 16.8 - - + -
51A LEU* 3.2 24.1 - - + +
53A LYS* 2.7 33.8 + - + -
54A ARG* 3.5 16.8 - - - -
55A LYS* 1.3 79.3 - - - +
57A LEU* 1.3 63.0 + - - +
58A VAL* 4.1 15.9 - - + -
67A PHE* 4.4 15.0 - + + -
70A LEU* 6.3 2.5 - - + -
71A ILE* 4.2 6.3 - - + -
74A ARG* 3.4 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.6 34.1 - - + -
32A TYR* 3.9 31.0 - - + -
35A ARG* 4.7 21.4 + - + +
36A VAL 3.5 3.1 - - - +
37A PRO* 4.0 20.2 - - + -
56A TYR* 1.3 72.2 - - - +
58A VAL* 1.3 62.0 + - - +
59A PRO* 3.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 4.0 2.9 - - - -
36A VAL* 2.5 45.5 + - + +
38A VAL* 4.2 15.3 - - + -
56A TYR* 4.1 11.4 - - + -
57A LEU* 1.3 75.9 - - - +
59A PRO* 1.3 82.2 - - + +
62A LEU* 3.7 21.5 - - + -
67A PHE* 3.5 33.2 - - + -
70A LEU* 6.3 0.4 - - + -
98A MET* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 4.0 7.0 - - - +
35A ARG* 4.2 23.3 - - + +
57A LEU 3.9 5.8 - - - +
58A VAL* 1.3 102.4 - - + +
60A SER* 1.3 64.0 + - - +
61A ASP* 3.2 16.2 + - - +
62A LEU* 3.4 24.3 + - + +
98A MET* 4.0 5.2 - - - +
----------------------------------------------------------
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