Contacts of the strand formed by residues 68 - 73 (chain A) in PDB entry 2FRV
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 PHE 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.2 27.1 - - - +
9A VAL 4.7 0.2 - - - +
10A VAL* 3.9 17.3 - - + -
63A ALA 3.8 13.7 - - - +
64A ILE* 3.5 36.1 - - + -
66A GLY 3.3 12.1 - - - -
67A ASP* 1.3 75.9 - - - +
69A VAL* 1.3 73.7 - - - +
70A CYS* 4.0 10.3 - - + -
99A VAL* 3.7 21.5 - - + -
102A LYS* 3.6 17.0 - - + -
103A ALA* 3.3 31.4 - - + -
104A LYS* 2.5 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 6.1 2.7 - - + -
8A SER 2.9 11.4 + - - +
9A VAL* 3.4 12.8 - - + +
10A VAL 3.0 24.8 + - - +
68A PHE* 1.3 79.7 - - - +
70A CYS* 1.3 70.7 - - - +
71A VAL* 4.1 6.7 - - + -
104A LYS* 4.7 6.1 - - + -
105A ALA* 3.4 29.8 - - + +
107A ILE* 4.4 20.2 - - + -
159A VAL* 5.5 3.6 - - + -
162A LEU* 4.6 7.0 - - + -
163A LEU* 4.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 3.5 8.5 - - - -
12A LEU* 4.3 5.6 - - - -
68A PHE* 4.0 6.5 - - + -
69A VAL* 1.3 73.7 - - - +
71A VAL* 1.3 59.7 + - - +
72A ILE* 3.7 29.4 - - - -
99A VAL* 4.0 23.1 - - - -
100A ALA* 4.3 6.7 - - - -
103A ALA* 3.6 21.9 - - + +
105A ALA 2.8 10.5 + - - +
106A VAL* 3.2 7.7 - - + +
107A ILE* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.6 26.9 - - + -
10A VAL 2.9 7.3 + - - +
11A TYR* 3.3 38.8 - - + -
12A LEU* 2.7 33.4 + - - +
69A VAL* 4.8 4.7 - - + -
70A CYS* 1.3 75.7 - - - +
72A ILE* 1.3 58.1 + - - +
73A GLU 4.1 0.2 - - - -
107A ILE* 3.4 13.7 - - + +
109A ILE* 4.0 10.8 - - + -
155A PHE* 3.7 33.4 - - + -
159A VAL* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.8 10.3 - - + -
14A ASN* 3.3 27.4 - - - +
70A CYS* 3.7 15.0 - - - -
71A VAL* 1.3 77.2 - - - +
73A GLU* 1.3 56.8 + - - +
74A GLY 4.1 6.3 - - - +
76A ILE* 4.9 1.1 - - + -
96A CYS* 4.4 9.9 - - - -
100A ALA* 4.1 20.9 - - + -
106A VAL* 3.9 22.4 - - + -
107A ILE 3.0 10.4 + - - +
108A ALA* 3.7 1.1 - - - -
109A ILE* 3.1 24.6 + - - -
113A ALA* 3.2 7.4 - - - +
131A VAL* 3.6 34.3 - - + -
135A LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 2.6 27.5 + - + -
12A LEU 2.9 9.6 + - - +
13A HIS* 3.7 0.2 - - - -
14A ASN* 2.9 29.3 + - - +
16A GLU* 2.9 32.0 - - + +
18A THR* 3.2 9.5 + - - -
20A CYS* 3.1 32.7 + - + +
21A SER* 2.4 36.6 + - - -
71A VAL 4.1 0.4 - - - -
72A ILE* 1.3 69.8 - - - +
74A GLY* 1.3 64.4 + - - +
109A ILE* 3.7 15.5 - - + +
267A SF4 4.0 2.3 - - - -
----------------------------------------------------------
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