Contacts of the strand formed by residues 16 - 23 (chain C) in PDB entry 1LFD
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 CYS 16 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.8 2.3 - - - +
16A CYS* 2.8 35.4 + - - +
17A CYS* 5.0 0.4 - - - -
18A ILE* 3.9 23.8 - - - -
35A LEU* 5.0 0.7 - - + -
14C GLY 3.6 12.1 - - - -
15C ASP* 1.3 84.5 - - - +
17C CYS* 1.3 64.1 + - - +
35C LEU* 3.7 24.2 - - + -
36C VAL 3.1 11.7 - - - +
37C THR* 3.9 20.4 - - - -
84C PHE* 3.9 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.1 12.8 - - - +
15A ASP* 4.3 7.2 - - - +
16A CYS* 4.4 0.4 - - - -
16C CYS* 1.3 77.5 - - - +
18C ILE* 1.3 61.1 + - - +
19C ILE* 3.7 20.4 + - - -
35C LEU* 3.7 4.4 - - - +
36C VAL* 2.9 32.0 + - - +
84C PHE* 3.8 23.8 - - + -
87C MET* 4.5 10.5 - - - -
93C TYR* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 2.8 30.2 + - - +
16A CYS* 4.2 5.2 - - - -
37A THR* 5.0 6.1 - - + -
17C CYS* 1.3 73.2 - - - +
19C ILE* 1.3 61.3 + - - +
20C ARG* 3.1 34.5 + - - +
33C SER* 3.8 5.2 - - - -
34C ILE 3.5 11.4 - - - +
35C LEU* 4.0 15.9 - - + -
93C TYR* 3.5 21.0 - - - +
236D ILE* 3.7 20.6 - - + -
264D TYR* 3.7 31.0 - - + -
267D MET* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C CYS* 3.9 20.9 - - - -
18C ILE* 1.3 79.9 - - - +
20C ARG* 1.3 64.9 + - - +
21C VAL* 5.0 3.4 - - + -
33C SER* 3.3 5.5 - - - -
34C ILE* 3.0 59.9 + - + -
36C VAL* 3.6 27.6 - - + -
45C VAL* 4.0 9.2 - - + -
65C LEU* 5.3 1.8 - - + -
83C VAL* 5.9 0.7 - - + -
87C MET* 4.6 3.8 - - + -
93C TYR* 3.6 14.8 - - + +
95C PHE* 4.0 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 5.2 4.6 - - - -
18C ILE* 3.1 34.6 + - - +
19C ILE* 1.3 74.0 - - - +
21C VAL* 1.3 56.7 + - - +
31C TYR* 3.3 36.8 - - + -
32C LYS 4.0 3.4 - - - -
33C SER* 2.7 19.3 + - - -
93C TYR* 2.8 13.6 + - - +
94C ASP* 3.4 24.6 - - + +
95C PHE* 2.7 34.3 + - - +
237D GLU* 2.9 37.9 + - - +
267D MET* 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.9 2.6 + - + -
20C ARG* 1.3 74.1 - - - +
22C SER* 1.3 64.0 + - - +
31C TYR* 3.4 1.1 - - - -
32C LYS* 2.9 43.8 + - + +
34C ILE* 4.3 22.9 - - + -
49C ALA* 3.9 22.0 - - + -
52C LYS* 5.3 0.2 - - + -
53C HIS* 2.9 35.2 + - + +
65C LEU* 4.8 6.3 - - + -
95C PHE* 3.4 9.6 - - + +
96C ILE 4.7 0.2 - - - -
97C LEU* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 1.3 76.9 - - - +
23C LEU* 1.3 74.0 + - - +
29C ASN* 4.6 4.4 + - - +
30C MET 3.0 28.1 + - - -
31C TYR* 4.3 3.1 - - - +
53C HIS* 4.2 3.6 - - - -
68C ILE* 5.8 3.1 - - - -
95C PHE 2.9 12.4 + - - -
96C ILE* 3.3 11.7 - - - -
97C LEU* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER* 1.3 85.6 + - - +
24C ASP* 1.3 59.6 + - - +
25C VAL* 2.9 37.4 + - + +
27C ASN* 4.4 20.0 - - - +
29C ASN* 5.4 2.0 + - - +
53C HIS* 3.7 38.7 - - + +
55C LEU* 3.7 36.1 - - + -
63C TYR* 5.3 1.3 - - + -
96C ILE* 4.6 2.5 - - - +
97C LEU* 3.8 28.7 - - + +
----------------------------------------------------------
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