Contacts of the strand formed by residues 71 - 75 (chain L) in PDB entry 2FGW
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 TYR 71 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L THR* 3.5 5.9 - - - -
23L CYS 2.8 38.7 + - - +
24L ARG* 4.8 0.7 + - - -
25L ALA* 5.1 2.5 - - + -
29L ILE* 3.2 21.8 - - + +
30L ASN 3.8 0.5 + - - -
31L ASN* 3.2 22.3 + - - -
33L LEU* 3.5 40.4 - - + -
35L TRP* 4.8 1.8 - - - +
51L THR* 3.6 27.6 - - + -
65L SER 3.3 20.4 - - - +
66L GLY* 3.7 4.7 - - - -
67L SER* 3.5 17.0 - - - -
68L GLY 2.9 38.1 + - - -
69L THR 3.9 3.4 - - - -
70L ASP* 1.3 81.2 - - - +
72L THR* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L THR* 3.5 28.5 - - + +
21L ILE 3.2 20.0 - - - +
22L THR* 4.0 11.7 - - + +
24L ARG* 5.8 0.5 + - - -
35L TRP* 4.0 8.7 + - - -
63L SER 3.8 0.2 - - - +
64L GLY* 3.4 8.1 - - - -
65L SER* 3.1 44.0 + - - -
66L GLY* 5.7 0.5 - - - -
70L ASP 5.6 0.3 - - - -
71L TYR* 1.3 79.2 + - - +
73L LEU* 1.3 62.5 + - - +
74L THR* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L VAL 3.5 0.4 - - - +
20L THR* 3.0 26.2 - - - -
21L ILE* 3.0 31.9 + - + +
35L TRP* 3.7 35.9 - - + -
47L LEU* 4.1 7.4 - - + -
48L ILE* 3.9 20.9 - - + -
62L PHE* 4.3 11.0 - - + -
63L SER 3.5 20.4 - - - +
72L THR* 1.3 71.3 - - - +
74L THR* 1.3 70.8 + - - +
75L ILE* 4.6 5.4 - - + -
86L TYR* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ARG* 3.8 33.8 + - - +
19L VAL 3.0 6.7 - - - +
20L THR* 3.0 19.8 + - - -
61L ARG 3.1 3.3 - - - +
62L PHE* 3.5 1.4 - - - -
63L SER* 3.1 45.4 + - - +
65L SER* 5.3 4.7 + - - -
72L THR* 4.6 6.7 - - - +
73L LEU* 1.3 76.6 + - - +
75L ILE* 1.3 61.7 + - - +
76L SER* 4.2 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ARG* 3.1 3.5 - - - -
19L VAL* 2.7 62.9 + - + +
21L ILE* 4.2 20.4 - - + -
61L ARG* 3.3 26.9 - - + +
62L PHE* 3.6 27.6 - - + +
73L LEU* 4.6 6.5 - - + -
74L THR* 1.3 72.1 - - - +
76L SER* 1.3 60.3 + - - +
77L SER 3.2 26.2 + - - +
78L LEU* 4.4 6.5 - - + -
82L ASP* 3.9 7.9 - - + +
86L TYR* 4.7 12.3 - - + +
104L VAL* 5.2 3.8 - - + -
----------------------------------------------------------
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