Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 3FN3
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 LYS 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 4.0 - - - -
59A MET* 2.8 55.5 + - + +
60A GLU* 2.8 24.6 + - + +
61A ASP* 1.3 78.7 - - - +
63A ASN* 1.3 65.4 + - - +
64A ILE* 3.2 5.0 + - - +
78A HIS* 3.2 46.4 - - + +
80A SER* 4.5 6.9 + - - -
81A TYR* 4.6 10.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.3 33.5 + - - +
57A TRP 3.1 10.5 + - - -
58A GLU* 4.6 0.4 - - - +
61A ASP 3.7 3.6 + - - -
62A LYS* 1.3 70.7 - - - +
64A ILE* 1.3 60.3 + - - +
65A ILE* 3.0 36.0 + - - -
66A GLN* 3.9 7.2 + - - +
73A ASP 4.7 0.9 - - - +
76A VAL* 3.6 26.9 - - + +
77A GLN* 3.5 21.1 + - - +
78A HIS* 3.0 32.4 + - - +
81A TYR* 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.1 9.5 + - + +
58A GLU* 3.8 6.7 - - - +
59A MET* 3.7 17.9 - - + +
62A LYS 3.9 7.2 - - - +
63A ASN* 1.3 76.8 - - - +
65A ILE* 1.3 61.8 + - - +
77A GLN* 2.9 32.6 + - - +
81A TYR* 3.8 30.3 - - + -
85A ALA* 3.4 28.3 - - + -
99A LEU* 3.8 23.3 - - + -
101A ILE* 4.2 1.1 - - + -
112A TYR* 3.4 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL 4.5 2.2 - - - +
56A TYR* 3.2 1.9 - - - -
57A TRP* 2.8 48.6 + - + +
63A ASN* 3.0 11.8 + - - +
64A ILE* 1.3 88.9 - - + +
66A GLN* 1.3 67.3 + - - +
67A PHE 4.2 4.3 - - - +
72A GLU* 5.0 14.4 - - + -
74A LEU* 5.8 4.0 - - + -
77A GLN* 4.2 5.2 - - - +
85A ALA 4.1 17.5 - - - +
86A ARG* 4.4 0.9 - - - -
87A LEU* 3.7 44.2 - - + +
99A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 6.0 2.0 - - + +
55A VAL 3.4 4.0 - - - +
56A TYR* 3.9 21.9 - - + +
63A ASN* 3.9 14.4 + - - +
65A ILE* 1.3 77.8 - - - +
67A PHE* 1.3 59.5 + - - +
68A VAL* 3.6 20.1 + - + +
72A GLU* 3.5 4.2 - - - +
73A ASP* 3.0 63.3 + - + +
76A VAL* 3.7 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.5 8.7 - - + -
53A LEU* 3.2 25.4 - - + +
54A ILE* 3.2 3.8 - - - -
55A VAL* 2.3 80.4 + - + +
65A ILE* 4.2 0.6 - - - +
66A GLN* 1.3 66.1 - - - +
68A VAL* 1.3 61.5 + - - +
70A GLY* 3.3 35.7 - - - -
71A GLU 2.9 26.7 - - - -
72A GLU* 3.5 20.6 - - + -
87A LEU* 3.6 20.6 - - + -
88A LEU 5.8 0.2 - - - -
89A LYS* 4.7 8.1 - - + -
92A LEU* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.8 3.4 - - - -
54A ILE* 3.6 29.6 - - + -
66A GLN* 3.6 21.8 + - + +
67A PHE* 1.3 80.3 - - - +
69A HIS* 1.3 90.6 + - + +
70A GLY 3.2 1.3 - - - -
71A GLU* 3.1 21.1 + - - +
73A ASP* 5.8 5.4 - - + +
----------------------------------------------------------
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