Contacts of the strand formed by residues 46 - 54 (chain B) in PDB entry 1CF5
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 ARG 46 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER 6.0 0.2 + - - -
40B THR* 6.2 1.6 - - - +
41B ILE* 4.0 23.7 - - + +
42B SER 2.9 3.1 + - - +
43B ASP* 3.3 28.1 + - - +
44B SER 3.5 0.2 - - - -
45B ARG* 1.3 80.6 - - - +
47B PHE* 1.3 93.9 + - + +
65B ASP* 3.4 26.2 + - - -
66B VAL* 3.0 29.4 + - - +
67B THR* 3.7 17.1 + - - +
87B PRO* 4.0 8.0 - - - +
89B GLU* 3.4 34.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP 4.6 1.0 + - - -
44B SER 5.3 2.5 - - - +
45B ARG* 3.4 2.7 + - - +
46B ARG* 1.3 123.0 - - + +
48B ILE* 1.3 67.1 + - - +
49B LEU* 5.0 3.4 - - + +
63B ALA* 5.1 0.4 - - + -
64B ILE 3.2 14.6 - - - +
65B ASP* 3.7 13.9 - - - -
72B VAL* 3.6 38.8 - - + -
87B PRO* 3.7 16.4 - - + -
89B GLU* 4.0 14.6 - - + -
90B ALA* 4.1 10.1 - - - -
93B ILE* 3.8 20.6 - - + +
94B LEU* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASP 6.2 0.9 - - - +
2B VAL* 4.3 10.3 - - + -
21B PHE* 4.0 29.2 - - + +
24B THR* 2.9 37.7 - - - +
25B LEU* 4.6 7.4 - - + +
26B PRO* 5.3 1.1 - - + -
45B ARG 5.1 2.0 - - - +
47B PHE* 1.3 77.1 - - - +
49B LEU* 1.3 64.1 + - - +
50B LEU* 4.2 2.2 - - + -
63B ALA* 3.5 3.6 - - - +
64B ILE* 2.7 52.9 + - + +
66B VAL* 3.4 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASP* 3.2 37.2 - - - +
2B VAL* 3.2 21.1 + - - +
47B PHE 5.0 3.4 - - - +
48B ILE* 1.3 86.6 - - - +
50B LEU* 1.3 64.1 + - - +
61B SER* 3.9 21.1 - - - +
62B VAL 3.4 4.0 - - - +
63B ALA* 4.2 18.2 - - + -
94B LEU* 4.5 13.7 - - + -
95B PHE* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASP* 5.0 0.2 - - - -
2B VAL* 3.4 25.8 - - + +
17B PHE* 4.1 14.1 - - + -
21B PHE* 4.1 21.1 - - + -
48B ILE* 4.7 2.2 - - + -
49B LEU* 1.3 77.2 - - - +
51B ASN* 1.3 59.8 + - - +
52B LEU* 3.8 20.0 + - + -
61B SER* 3.6 6.6 + - - -
62B VAL* 2.8 40.3 + - + +
64B ILE* 3.8 32.3 - - + -
156B THR* 4.0 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASP* 3.8 17.0 - - - +
2B VAL 2.7 10.6 + - - +
3B ASN* 3.4 19.2 + - - +
4B PHE 2.8 24.6 + - - +
49B LEU 3.8 0.4 + - - -
50B LEU* 1.3 71.4 - - - +
52B LEU* 1.3 60.6 + - - +
53B THR 4.1 0.2 + - - -
59B THR* 3.2 20.5 - - - +
60B ILE 4.3 2.2 - - - +
61B SER* 5.0 5.4 - - - +
1D NAG 1.5 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.5 31.9 - - + +
6B LEU* 5.8 0.4 - - + -
17B PHE* 4.7 9.4 - - + -
50B LEU* 4.1 18.6 - - + -
51B ASN* 1.3 76.7 + - - +
53B THR* 1.3 61.1 + - - +
58B GLU 4.0 0.3 - - - +
59B THR* 3.2 3.6 - - - +
60B ILE* 2.8 48.3 + - + +
62B VAL* 3.7 17.9 - - + -
130B LEU* 5.2 5.2 - - + -
134B ILE* 4.1 18.8 - - + +
152B LEU* 3.6 31.2 - - + -
156B THR* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE 3.2 5.9 + - - +
5B ASP* 3.7 26.2 - - - +
6B LEU* 2.9 31.9 + - - +
51B ASN 4.8 0.2 + - - -
52B LEU* 1.3 73.6 - - - +
54B SER* 1.3 72.3 + - - +
57B TYR* 3.5 27.1 - - + +
58B GLU 3.4 3.8 - - - -
59B THR* 2.9 22.2 + - - +
134B ILE* 4.0 3.1 - - - +
1D NAG 3.4 22.9 + - - -
2D NAG 5.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 3.8 5.9 - - - +
6B LEU* 3.7 4.5 - - - -
7B SER* 4.0 0.5 - - - -
53B THR* 1.3 82.8 - - - +
55B TYR* 1.3 65.2 + - - +
56B ALA* 3.0 12.6 + - - -
57B TYR 3.0 13.5 + - - -
58B GLU* 2.7 38.9 + - - -
131B SER* 2.9 27.1 - - - -
134B ILE* 3.9 14.9 - - - +
135B THR* 4.0 0.4 - - - -
----------------------------------------------------------
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