Contacts of the strand formed by residues 6 - 14 (chain F) in PDB entry 1RFU
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 6 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.8 31.3 - - - +
17B GLY 5.8 0.2 - - - +
277B LYS* 5.3 8.3 - - - +
4F GLU 4.3 0.2 - - - -
5F CYS* 1.3 73.4 - - - +
7F VAL* 1.3 63.7 + - - +
8F LEU 4.3 0.2 - - - -
34F GLU* 3.2 34.8 + - + +
36F ASP* 2.9 28.3 + - - +
74F VAL 5.0 3.1 + - - -
76F GLN 3.2 26.5 + - - +
77F TYR* 3.4 23.8 - - + -
78F ASP* 2.9 39.1 + - - +
79F TYR 3.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG* 1.3 80.5 - - - +
8F LEU* 1.3 63.0 + - - +
9F SER* 3.3 5.3 + - - +
28F LEU* 4.3 14.6 - - + -
33F PHE* 3.8 36.8 - - + -
34F GLU 2.8 10.5 + - - +
35F VAL* 3.6 4.0 - - + +
36F ASP 2.9 25.6 + - - -
77F TYR* 3.9 3.6 - - - -
79F TYR* 3.9 20.2 - - + -
81F LEU* 4.2 15.9 - - + -
242F LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.7 2.5 - - + -
7F VAL* 1.3 70.5 - - - +
9F SER* 1.3 56.5 + - - +
10F ILE* 3.7 20.8 + - + +
36F ASP* 3.4 15.7 - - + +
38F VAL* 3.9 25.4 - - + -
66F TYR* 5.1 6.5 - - + -
69F LEU* 5.1 2.9 - - + -
77F TYR* 3.4 46.7 - - + +
79F TYR 3.3 13.3 + - - +
80F VAL* 3.5 12.2 - - + +
81F LEU 3.1 21.7 + - - +
97F ILE* 4.7 9.9 - - + -
101F LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 3.3 5.3 + - - -
8F LEU* 1.3 72.6 - - - +
10F ILE* 1.3 59.8 + - - +
11F GLN* 2.8 22.2 + - - -
21F ASN* 2.6 28.3 + - - +
24F ALA* 4.6 1.5 - - - +
28F LEU* 5.4 2.7 - - - -
35F VAL* 4.3 13.5 - - - -
36F ASP 2.8 11.2 + - - +
37F ALA* 3.4 2.6 - - - -
38F VAL* 2.9 25.8 + - - +
81F LEU* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 4.0 33.2 - - + +
9F SER* 1.3 77.1 + - - +
11F GLN* 1.3 61.7 + - - +
38F VAL* 3.4 20.9 - - + +
40F SER* 4.9 0.8 - - - -
62F LEU* 5.0 9.4 - - + -
80F VAL* 5.4 1.8 - - + -
81F LEU 2.7 11.4 + - - +
82F THR* 3.3 10.6 - - + -
83F GLY 2.9 25.5 + - - +
84F TYR 4.9 0.2 - - - +
85F THR* 5.6 0.9 + - - +
90F PHE* 3.5 36.6 - - + -
94F VAL* 4.3 28.0 - - + -
97F ILE* 5.4 6.3 - - + -
98F VAL* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 2.8 23.7 + - - +
10F ILE* 1.3 82.1 - - - +
12F SER* 1.3 63.6 + - - +
20F GLY* 3.7 12.0 - - - +
21F ASN* 2.9 25.0 + - - +
24F ALA* 3.4 24.4 - - - +
38F VAL 3.1 2.0 + - - -
39F ASN* 3.1 5.5 - - - -
40F SER* 2.9 27.0 + - - -
81F LEU* 3.9 13.9 - - - +
82F THR 4.3 2.0 - - - -
83F GLY* 3.6 17.3 - - - +
84F TYR 4.0 8.3 - - - +
113F ASP* 5.9 0.7 - - - +
235F ASP* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLN* 1.3 75.8 - - - +
13F HIS* 1.3 58.9 + - - +
19F VAL* 4.2 0.7 - - - +
20F GLY* 3.0 15.6 - - - -
21F ASN* 2.5 33.6 + - - +
40F SER* 2.9 3.9 + - - -
41F VAL* 3.1 28.0 - - - -
84F TYR* 3.5 20.6 + - - +
5401F PLP 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS* 5.5 1.3 + - - -
37B ALA* 3.0 33.8 + - + -
39B ASN* 3.3 29.7 + - - -
12F SER* 1.3 75.2 - - - +
14F VAL* 1.3 73.4 + - - +
19F VAL 5.0 0.2 - - - -
21F ASN* 4.9 1.0 - - - +
22F ARG* 3.9 30.6 + - - +
39F ASN* 3.5 26.2 + - + +
41F VAL* 2.9 17.7 + - - +
42F GLN* 3.2 20.6 + - + -
43F PHE* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F HIS* 1.3 87.3 + - - +
15F VAL* 1.3 66.5 + - - +
16F ARG 3.1 22.0 - - - +
17F GLY 3.4 20.4 - - - +
19F VAL* 3.5 30.5 - - + +
22F ARG* 3.3 23.4 - - + +
43F PHE* 3.3 5.2 - - + +
45F ASN* 3.6 29.6 - - - +
46F HIS* 4.0 1.8 - - - +
5401F PLP 4.4 7.4 - - + -
----------------------------------------------------------
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