Contacts of the helix formed by residues 53 - 57 (chain B) in PDB entry 5DAH
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 GLN 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU 4.2 8.2 - - - +
37B ASN* 3.1 11.7 + - - +
38B PRO* 3.1 35.6 + - + +
40B VAL* 4.4 3.8 - - - +
51B VAL 3.8 0.2 + - - -
52B HIS* 1.3 71.7 - - - +
54B ALA* 1.3 57.6 - - + +
56B TYR 3.5 0.2 + - - -
57B GLY* 3.0 25.5 + - - -
58B ILE* 3.0 46.9 + - + +
59B VAL 3.5 17.4 + - - -
60B GLN* 4.4 0.4 - - - +
61B VAL* 3.5 24.2 - - + +
20C LEU 6.0 3.6 - - - +
22C THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 2.9 28.6 + - - +
53B GLN* 1.3 77.1 - - + +
55B CYS* 1.3 61.6 + - - +
56B TYR 3.4 0.4 - - - -
57B GLY 4.2 1.3 - - - -
120B MET* 3.8 0.9 - - - +
20C LEU* 4.9 11.7 - - + +
21C ALA 3.9 20.9 - - - +
22C THR* 3.3 15.8 - - - +
23C LYS* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B CYS* 3.8 1.6 - - - -
27B VAL* 3.8 19.2 - - + +
28B CYS* 3.7 4.9 - - - -
37B ASN* 5.7 0.7 - - - -
51B VAL* 4.4 1.8 - - + -
52B HIS* 2.9 21.7 + - - +
54B ALA* 1.3 79.8 - - - +
56B TYR* 1.3 59.2 + - - +
103B VAL* 3.5 26.0 - - - +
120B MET* 3.6 6.4 - - - +
301B ZN 2.3 37.5 - - - -
23C LYS* 3.6 33.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 5.2 0.7 - - + -
51B VAL* 3.5 23.6 - - + -
52B HIS 3.3 5.1 + - - +
55B CYS* 1.3 77.9 - - - +
57B GLY* 1.3 63.7 + - - +
58B ILE* 3.7 11.7 - - + -
66B TRP* 3.5 33.2 - + - -
68B CYS* 3.4 10.3 - - + +
69B ARG* 2.8 36.0 + - + +
70B LYS 4.3 0.3 + - - -
91B ALA* 3.6 34.3 - - + -
92B LEU 2.8 22.7 + - - -
93B LYS* 3.0 48.5 + - + +
103B VAL* 4.1 7.0 - - + -
120B MET* 4.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN 3.0 7.4 + - - -
54B ALA 4.2 0.4 - - - -
55B CYS 3.7 1.2 - - - -
56B TYR* 1.3 79.1 - - - +
58B ILE* 1.3 64.7 + - - +
59B VAL* 3.4 5.7 + - - +
69B ARG* 5.6 3.1 + - - -
93B LYS* 5.0 0.2 + - - -
118B SER 3.5 20.0 - - - +
119B THR* 3.5 25.6 - - - +
120B MET* 3.7 12.7 - - - -
22C THR* 4.4 5.4 - - - -
----------------------------------------------------------
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