Contacts of the strand formed by residues 36 - 41 (chain F) in PDB entry 6CP3
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 ALA 36 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ASN* 1.3 72.4 - - - +
37F LEU* 1.3 64.2 + - - +
47F VAL* 4.4 8.7 - - + -
48F LEU 3.3 7.9 - - - +
49F GLU* 4.7 0.7 - - - +
78F ASP* 4.5 0.5 - - - +
79F THR* 2.3 44.7 + - + +
80F GLY 4.3 0.7 + - - -
81F GLY 2.8 14.6 + - - +
82F PRO 4.1 6.3 - - - +
83F ILE* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 4.1 16.4 - - + -
25F PHE* 4.2 13.7 - - + -
31F PRO* 4.1 13.7 - - + -
35F ASN 3.8 0.8 + - - -
36F ALA* 1.3 77.8 - - - +
38F GLU* 1.3 64.4 + - - +
47F VAL* 3.5 6.6 - - - +
48F LEU* 2.9 39.5 + - + +
50F VAL* 3.9 23.8 - - + -
59F VAL* 4.5 0.9 - - + -
61F THR* 4.2 8.5 - - + -
76F VAL* 3.8 23.8 - - + -
77F LEU 3.4 13.5 - - - +
78F ASP* 3.4 29.4 - - + +
79F THR* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 1.3 76.1 - - - +
39F ILE* 1.3 66.7 + - - +
40F LYS* 3.7 25.2 + - - +
45F LYS* 3.4 29.1 + - + +
46F LEU 3.3 13.7 - - - +
47F VAL* 4.6 7.3 - - + +
48F LEU* 4.6 0.4 - - - +
77F LEU* 2.8 51.3 + - + +
79F THR* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F VAL* 3.8 27.4 - - + -
38F GLU* 1.3 81.3 - - - +
40F LYS* 1.3 77.1 + - - +
41F THR* 3.3 11.2 + - + +
45F LYS* 3.4 3.1 - - - -
46F LEU* 2.9 38.4 + - + +
48F LEU* 3.7 26.9 - - + -
70F LEU* 4.4 15.7 - - + -
74F GLU* 4.0 17.9 - - + +
75F LYS 3.8 19.1 - - - +
76F VAL* 3.9 12.3 - - + -
77F LEU* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLU* 3.7 22.2 + - - +
39F ILE* 1.3 71.0 - - - +
41F THR* 1.3 63.2 + - - +
42F PRO* 4.7 0.5 - - - +
44F GLY 3.7 9.0 - - - +
45F LYS* 4.5 11.2 - - + +
74F GLU* 3.3 18.9 - - - +
75F LYS* 4.9 4.6 + - + -
77F LEU* 3.5 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ILE* 3.5 22.7 - - + +
40F LYS* 1.3 77.6 - - - +
42F PRO* 1.3 69.1 - - - +
43F GLN* 3.5 11.3 + - - +
44F GLY* 2.9 45.0 + - - +
45F LYS* 3.4 4.0 + - - -
46F LEU* 3.7 28.9 - - + +
70F LEU* 4.6 10.8 - - + -
74F GLU* 4.7 0.7 - - - -
----------------------------------------------------------
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