Contacts of the strand formed by residues 60 - 66 (chain B) in PDB entry 3FA6
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 THR 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL 2.9 11.6 + - - -
59A ARG* 3.1 37.3 + - + +
60A THR 3.0 23.2 + - - -
53B LYS* 3.7 34.1 - - + -
54B VAL 3.3 5.8 - - - +
55B SER* 4.0 11.7 + - - +
56B THR 4.9 2.3 + - - -
59B ARG* 1.3 77.2 + - - +
61B THR* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.2 19.3 - - - +
62A GLU* 6.2 0.2 - - - -
52B ILE 4.6 0.4 - - - -
53B LYS* 3.2 8.0 - - - +
54B VAL* 2.9 56.0 + - + +
59B ARG* 4.8 13.9 - - + -
60B THR* 1.3 77.9 - - - +
62B GLU* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.0 32.6 + - - +
60A THR 2.9 10.0 + - - +
61A THR* 2.7 38.1 + - + +
62A GLU* 2.9 30.3 + - - +
73A GLU* 6.0 0.3 - - - +
74A GLN* 4.2 12.0 + - - +
51B TYR* 2.6 39.4 + - + +
52B ILE 3.4 6.7 - - - -
53B LYS* 4.2 4.3 - - + -
60B THR* 4.6 1.1 - - + -
61B THR* 1.3 80.4 - - - +
63B ILE* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.4 30.5 - - + +
64A ASN* 3.6 9.9 - - - +
51B TYR* 3.4 6.9 - - - -
52B ILE* 2.9 55.4 + - + +
62B GLU* 1.3 75.1 - - - +
64B ASN* 1.3 67.8 + - - +
65B PHE* 4.5 8.5 - - + -
71B PHE* 4.4 7.0 - - + -
72B GLU 3.6 12.6 - - - +
73B GLU* 3.5 41.5 - - + +
138B LSR 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU 3.5 2.2 + - - -
63A ILE* 3.2 18.8 - - - +
64A ASN* 2.9 70.5 + - - +
71A PHE* 3.6 17.9 - - - +
72A GLU 3.3 25.3 + - - +
73A GLU* 6.1 0.6 - - - +
50B PHE 3.2 15.5 - - - +
51B TYR* 4.3 3.6 - - + -
63B ILE* 1.3 77.7 - - - +
65B PHE* 1.3 70.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 4.8 4.7 - - - -
49B THR* 3.6 2.3 - - - -
50B PHE* 2.8 72.9 + + + +
52B ILE* 3.9 24.0 - - + -
63B ILE* 4.5 9.2 - - + -
64B ASN* 1.3 86.1 + - - +
66B LYS* 1.3 68.5 + - - +
67B VAL* 4.5 1.6 - - + -
71B PHE* 3.6 39.7 - + + -
73B GLU* 6.0 0.2 - - - -
85B VAL* 3.9 28.0 - - + -
93B MET* 4.4 4.3 - - - -
109B TRP* 3.8 24.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 5.6 1.3 - - - +
70A GLU 5.9 0.9 - - - +
48B ASP* 3.3 31.0 + - - +
49B THR* 3.7 25.5 - - + +
65B PHE* 1.3 82.7 - - - +
67B VAL* 1.3 76.7 + - - +
68B GLY 3.2 0.7 + - - -
69B GLU* 3.2 60.6 + - + +
71B PHE* 5.0 1.6 - - - +
85B VAL* 5.2 0.7 + - - +
----------------------------------------------------------
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