Contacts of the strand formed by residues 68 - 73 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I SER* 3.2 27.8 - - - +
10I VAL* 3.9 18.2 - - + -
63I ALA 3.8 13.0 - - - +
64I ILE* 3.5 35.9 - - + -
66I GLY 3.3 11.6 + - - -
67I ASP* 1.3 75.2 - - - +
69I VAL* 1.3 75.0 + - - +
70I CYS* 4.0 10.5 - - + -
99I VAL* 3.7 21.8 - - + -
102I LYS* 3.6 17.5 - - + -
103I ALA* 3.3 30.5 - - + -
104I LYS* 2.5 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I PRO* 6.1 2.7 - - + -
8I SER 2.9 11.2 + - - +
9I VAL* 3.4 13.2 - - + +
10I VAL 3.0 24.9 + - - +
68I PHE* 1.3 81.1 - - - +
70I CYS* 1.3 71.1 - - - +
71I VAL* 4.8 6.1 - - + -
104I LYS* 4.7 6.3 - - + -
105I ALA* 3.4 28.9 - - + +
107I ILE* 4.4 19.7 - - + -
159I VAL* 5.5 3.6 - - + -
162I LEU* 4.6 8.1 - - + -
163I LEU* 4.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL 3.5 8.1 - - - -
12I LEU* 4.3 6.1 - - - -
68I PHE* 4.0 6.3 - - + -
69I VAL* 1.3 75.5 - - - +
71I VAL* 1.3 60.0 + - - +
72I ILE* 3.7 28.5 - - - -
99I VAL* 4.0 22.7 - - - -
100I ALA* 4.3 6.7 - - - -
103I ALA* 3.6 21.7 - - + +
105I ALA 2.8 10.0 + - - +
106I VAL* 3.2 7.0 - - + +
107I ILE* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 3.6 26.5 - - + -
10I VAL 2.9 8.0 + - - +
11I TYR* 3.3 39.5 - - + -
12I LEU* 2.7 33.4 + - - +
69I VAL* 4.8 5.4 - - + -
70I CYS* 1.3 74.5 - - - +
72I ILE* 1.3 57.1 - - - +
107I ILE* 3.4 13.0 - - + +
109I ILE* 4.0 10.8 - - + -
155I PHE* 3.7 33.9 - - + -
159I VAL* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 3.8 9.0 - - + -
14I ASN* 3.3 27.6 - - - +
70I CYS* 3.7 14.6 - - - -
71I VAL* 1.3 77.2 - - - +
73I GLU* 1.3 55.8 + - - +
74I GLY 4.1 6.3 - - - +
76I ILE* 4.9 1.3 - - + -
96I CYS* 4.4 9.4 - - - -
100I ALA* 4.1 22.0 - - + -
106I VAL* 3.9 20.9 - - + -
107I ILE 3.0 10.6 + - - +
108I ALA* 3.7 0.6 - - - -
109I ILE* 3.1 25.4 + - - -
113I ALA* 3.2 7.3 - - - +
131I VAL* 3.6 35.0 - - + -
135I LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 2.6 27.6 + - + -
12I LEU 2.9 9.8 + - - +
13I HIS* 3.7 0.6 - - - -
14I ASN* 2.9 28.8 + - - +
16I GLU* 2.9 31.8 - - + +
18I THR* 3.2 9.5 + - - -
20I CYS* 3.1 32.1 + - + -
21I SER* 2.4 36.4 + - - -
71I VAL 4.1 0.2 - - - -
72I ILE* 1.3 70.6 - - - +
74I GLY* 1.3 64.3 + - - +
109I ILE* 3.7 15.7 - - + +
267I SF4 4.0 2.9 - - - -
----------------------------------------------------------
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