Contacts of the strand formed by residues 44 - 55 (chain V) in PDB entry 3FKS
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 GLY 44 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40V LYS* 4.5 6.1 - - - +
41V THR* 2.9 23.8 + - - +
42V PRO 3.2 1.2 - - - -
43V GLN* 1.3 81.7 - - - +
45V LYS* 1.3 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V GLU* 3.4 34.4 + - + +
39V ILE 3.5 11.2 - - - +
40V LYS* 5.3 0.9 - - - -
41V THR* 3.0 11.1 + - - -
43V GLN* 5.5 0.4 - - - +
44V GLY* 1.3 75.5 - - - +
46V LEU* 1.3 62.2 + - - +
47V VAL* 4.2 8.0 + - + +
65V ASP* 5.2 6.1 - - - +
99V ILE* 4.7 14.4 - - - +
101V GLU* 3.1 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V GLU* 3.4 4.7 - - - +
39V ILE* 2.9 50.7 + - + +
41V THR* 3.7 19.6 + - + -
45V LYS* 1.3 74.5 - - - +
47V VAL* 1.3 70.6 + - - +
48V LEU* 5.2 3.1 - - + -
63V ALA* 5.4 0.2 - - + -
65V ASP* 3.7 29.8 - - + +
66V GLY 3.5 21.5 - - - +
67V THR* 3.9 18.6 - - + -
70V LEU* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V ALA* 5.2 2.7 - - + -
37V LEU 3.4 10.8 - - - +
38V GLU* 4.5 15.3 - - + +
45V LYS* 4.6 12.1 - - + +
46V LEU* 1.3 85.2 - - - +
48V LEU* 1.3 72.7 + - - +
49V GLU* 6.0 0.2 - - + -
63V ALA* 3.8 3.3 - - - +
64V MET* 3.1 47.0 + - + +
65V ASP* 4.4 3.5 + - - +
83V ILE* 4.4 14.8 - - + -
99V ILE* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V VAL* 5.3 0.7 - - + -
21V VAL* 3.9 34.5 - - + -
23V VAL* 4.0 15.0 - - + -
36V ALA* 3.9 2.1 - - - -
37V LEU* 2.8 40.1 + - + +
39V ILE* 3.8 26.5 - - + -
46V LEU* 4.2 2.2 + - + -
47V VAL* 1.3 84.1 - - - +
49V GLU* 1.3 63.0 + - - +
61V THR* 3.3 28.0 - - + +
62V ILE 3.8 2.9 - - - -
63V ALA* 3.9 26.9 - - + +
64V MET* 4.7 0.7 - - - -
67V THR* 4.9 3.6 - - + -
76V VAL* 4.7 5.2 - - + -
83V ILE* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V LEU* 3.7 11.7 - - - +
35V ASN 3.5 12.6 - - - +
36V ALA* 5.3 0.7 - - - -
37V LEU* 4.8 0.7 - - - +
48V LEU* 1.3 77.6 - - - +
50V VAL* 1.3 73.1 - - - +
51V ALA* 4.4 0.9 - - - +
61V THR* 3.1 22.1 - - - -
62V ILE* 3.1 21.3 + - + +
64V MET* 4.4 11.1 - - - +
83V ILE* 3.6 23.2 - - + +
118V HIS* 3.1 21.5 - - - -
231V ARG* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31V PRO* 4.1 13.0 - - + +
32V ALA 3.2 29.4 - - - +
33V ILE* 3.5 8.5 - - - +
34V LEU* 3.1 22.5 + - - +
35V ASN* 3.2 25.9 + - + +
37V LEU* 4.3 20.0 - - + -
49V GLU* 1.3 78.2 - - - +
51V ALA* 1.3 62.2 + - - +
52V GLN 4.3 4.9 - - - +
53V HIS* 4.4 2.9 - - + +
59V VAL* 4.2 26.7 - - + -
61V THR* 3.7 6.9 - - + +
231V ARG* 5.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S GLY* 4.7 3.8 - - - -
38S ASP* 5.0 1.7 + - - +
81S ASP* 4.9 3.8 - - - +
33V ILE* 3.5 20.5 - - - +
49V GLU 4.4 0.7 - - - +
50V VAL* 1.3 74.4 - - - +
52V GLN* 1.3 67.3 + - + +
60V ARG 2.8 16.7 + - - +
62V ILE* 4.3 15.9 - - + -
272V LEU* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S VAL 3.5 13.7 - - - +
37S GLY* 3.6 9.7 - - - -
38S ASP* 3.5 25.7 - - - +
33V ILE* 4.2 5.7 - - - +
50V VAL* 4.3 0.6 - - - +
51V ALA* 1.3 84.7 - - + +
53V HIS* 1.3 63.1 + - - +
54V LEU* 3.1 30.9 + - + +
59V VAL* 3.5 3.0 - - - +
60V ARG* 3.0 56.3 + - + +
272V LEU* 5.0 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S ALA* 3.3 4.4 - - - +
36S VAL* 2.9 41.6 + - + +
85S LYS* 4.1 16.2 - - + -
86S GLU* 3.6 29.6 + - + +
30V LEU* 4.2 16.1 - - + +
31V PRO 3.0 29.6 + - - -
32V ALA* 3.3 19.7 - - - -
33V ILE* 3.3 24.4 - - + +
50V VAL* 4.5 2.0 - - + -
52V GLN* 1.3 70.5 - - - +
54V LEU* 1.3 65.4 + - - +
55V GLY 3.1 3.5 + - - +
58V THR 4.0 0.7 - - - +
59V VAL* 3.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S LEU* 5.1 2.9 - - - +
35S ALA* 3.7 11.5 - - - +
42S ARG* 5.6 3.3 + - - -
22V ASP* 3.2 37.2 - - - +
52V GLN* 3.1 33.8 + - - +
53V HIS* 1.3 70.8 - - - +
55V GLY* 1.3 61.0 + - - +
58V THR* 2.9 24.2 + - + +
60V ARG* 3.6 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S LEU* 3.4 24.2 - - - -
86S GLU* 3.5 8.2 + - - -
53V HIS 3.1 5.3 - - - -
54V LEU* 1.3 82.8 - - - +
56V GLU* 1.3 75.6 + - - +
57V ASN 3.3 2.5 - - - -
58V THR* 3.4 15.8 + - - +
----------------------------------------------------------
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