Contacts of the helix formed by residues 52 - 58 (chain B) in PDB entry 4CRU
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 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 4.3 24.5 - - + -
26B ILE* 4.3 10.1 - - + -
42B LEU* 3.9 31.9 - - + +
45B LYS* 4.4 5.6 - - + +
46B ARG* 4.0 26.7 - - + +
49B VAL* 3.0 23.7 + - + +
50B PRO 3.3 1.0 - - - -
51B ASP* 1.3 78.9 + - - +
53B ALA* 1.3 62.8 + - - +
55B MET* 3.2 8.0 + - + +
56B LEU* 2.9 43.2 + - + +
96B LEU* 4.2 9.4 - - + -
99B CYS* 4.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO 4.7 1.0 + - - -
51B ASP 3.2 0.2 - - - -
52B LEU* 1.3 77.9 - - - +
54B PRO* 1.3 72.2 - - + +
56B LEU* 3.2 3.9 + - - +
57B TRP* 2.9 23.4 + - - +
99B CYS* 3.5 28.3 - - - +
100B VAL* 3.8 10.6 - - - +
103B HIS* 3.3 30.1 - - + -
106B THR* 3.7 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1548A TYR* 3.6 21.8 - - - +
1553A MET* 4.4 1.3 - - - +
51B ASP* 3.3 28.5 - - + +
53B ALA* 1.3 96.1 - - + +
55B MET* 1.3 55.8 + - + +
58B HIS* 2.9 39.0 + - + +
103B HIS* 3.7 19.1 - - + +
105B GLU* 4.0 19.1 - - + +
106B THR* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1553A MET* 4.1 8.3 - - - +
1554A PRO* 4.2 10.3 - - + -
1557A ILE* 3.7 22.9 - - + +
19B ARG* 3.6 24.7 - - - +
22B ILE* 4.1 19.1 - - + -
23B TYR* 3.7 18.2 - - + -
26B ILE* 3.9 9.2 - - + +
49B VAL* 4.0 11.0 - - + -
51B ASP* 3.3 35.4 + - + +
52B LEU* 3.2 16.2 + - + +
54B PRO* 1.3 78.8 - - + +
56B LEU* 1.3 52.0 + - - +
59B SER* 2.8 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.2 20.0 - - + -
29B LEU* 4.3 10.1 - - + -
42B LEU* 4.5 5.8 - - + -
52B LEU* 2.9 40.2 + - + +
53B ALA 3.6 3.1 - - - +
55B MET* 1.3 74.2 - - - +
57B TRP* 1.3 65.4 + - - +
59B SER* 3.2 14.6 + - - +
62B THR* 3.2 36.0 - - + +
63B ILE* 3.9 6.9 - - + +
66B LEU* 5.2 1.8 - - + -
96B LEU* 4.0 41.7 - - + +
99B CYS* 4.3 5.2 - - - -
100B VAL* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1422A GLN* 5.9 1.6 - - + -
1423A ILE* 3.9 18.6 - - + -
1426A LYS* 2.8 62.9 + - + +
53B ALA 2.9 17.0 + - - +
54B PRO 3.3 2.2 + - - +
56B LEU* 1.3 78.7 - - - +
58B HIS* 1.3 80.5 + + + +
59B SER 3.6 0.2 + - - -
63B ILE* 3.6 30.6 - - + +
100B VAL* 3.7 15.9 - - + +
106B THR* 3.6 19.3 - - + -
109B ALA* 3.5 46.8 - - + +
110B PHE* 3.8 9.4 - - - -
113B ALA* 4.1 5.4 - - + -
115B ILE* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426A LYS* 4.1 10.5 + - + +
1545A VAL* 6.2 3.1 - - + +
1548A TYR* 3.5 43.3 + + + -
1549A GLN* 3.0 29.9 + - - +
1553A MET* 3.6 15.6 - - + +
1559A LEU* 3.9 8.8 - - - +
54B PRO* 2.9 32.5 + - + +
57B TRP* 1.3 98.9 - + + +
59B SER* 1.3 65.3 + - - +
105B GLU* 5.0 6.5 + - - +
106B THR* 4.7 5.0 - - + +
----------------------------------------------------------
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