Contacts of the strand formed by residues 60 - 68 (chain A) in PDB entry 2FE4
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 ARG 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.4 6.1 - - - -
56A TYR* 3.4 12.1 - - - -
57A LEU* 2.9 38.7 + - - +
58A GLU* 3.6 8.5 - - + +
59A ASP* 1.3 81.1 - - - +
61A THR* 1.3 77.7 + - - +
62A VAL* 3.1 16.4 - - + +
63A ARG* 2.5 37.0 - - - +
175A LEU* 3.3 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.0 20.1 - - + +
55A MET 3.4 7.0 - - - +
56A TYR* 5.1 7.2 - - + -
60A ARG* 1.3 93.3 + - - +
62A VAL* 1.3 64.0 + - - +
63A ARG* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.9 24.2 - - + -
53A LYS 3.9 0.2 - - - +
54A THR* 3.6 2.2 - - - -
55A MET* 3.0 39.2 + - + +
57A LEU* 3.6 30.5 - - + -
60A ARG* 3.1 35.9 - - - +
61A THR* 1.3 73.9 - - - +
63A ARG* 1.3 69.0 + - - +
64A LEU* 3.7 20.7 + - + +
171A ALA* 4.5 1.3 - - + -
175A LEU* 4.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.6 26.9 + - - +
52A SER* 5.8 2.2 - - - +
53A LYS 3.3 7.6 - - - +
54A THR* 3.8 21.7 - - - +
60A ARG* 2.5 34.2 - - - +
61A THR* 3.5 14.1 + - - -
62A VAL* 1.3 88.5 - - - +
64A LEU* 1.3 62.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.5 38.4 - - + +
16A LEU* 3.4 29.6 - - + -
33A PHE* 4.7 4.7 - - + -
52A SER* 3.3 7.3 - - - -
53A LYS* 2.6 40.0 + - + +
55A MET* 3.6 26.9 - - + -
62A VAL* 3.7 15.3 - - + +
63A ARG* 1.3 78.6 - - - +
65A GLN* 1.3 62.3 + - - +
66A LEU* 3.9 12.5 - - + +
167A PHE* 4.2 13.2 - - + +
170A VAL* 5.2 0.2 - - + -
171A ALA* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE 3.1 14.5 + - - +
15A LYS* 2.9 41.3 + - + +
16A LEU* 2.8 31.4 + - - +
50A PHE* 3.2 39.0 - - + -
51A LEU 3.6 2.0 - - - -
52A SER* 4.6 1.3 - - - +
64A LEU* 1.3 73.9 - - - +
66A LEU* 1.3 61.3 + - - +
67A TRP* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.5 31.4 - - + +
18A PHE* 4.8 2.5 - - + -
30A ILE* 4.1 25.4 - - + +
33A PHE* 4.0 16.8 - - + -
34A MET* 3.8 34.3 - - + -
50A PHE* 3.4 5.4 - - - +
51A LEU* 2.6 47.9 + - + +
52A SER 5.5 0.2 - - - -
53A LYS* 5.3 1.1 - - + +
64A LEU* 3.9 17.5 - - + +
65A GLN* 1.3 78.5 - - - +
67A TRP* 1.3 61.9 + - - +
68A ASP* 4.1 0.7 + - - +
167A PHE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 4.4 14.0 - - + +
16A LEU 2.7 18.4 + - - -
17A VAL* 3.4 25.1 - - + -
18A PHE* 2.9 34.3 + - - +
30A ILE* 4.4 2.7 - - - -
49A ASP* 3.6 31.2 - - + -
50A PHE* 4.0 14.6 - + + -
65A GLN* 3.0 57.7 + - + +
66A LEU* 1.3 74.7 - - - +
68A ASP* 1.3 60.1 + - - +
69A THR* 4.1 4.2 + - + +
82A TYR* 3.7 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.8 0.8 - - - +
26A LYS* 4.0 14.4 - - - +
27A THR* 2.4 38.8 + - - +
30A ILE* 3.7 20.7 - - + +
45A THR* 3.8 15.8 + - - +
46A ILE* 5.6 4.0 - - - -
47A GLY 5.9 0.3 + - - -
49A ASP* 3.8 26.9 + - - +
50A PHE* 6.1 0.4 - - - -
51A LEU* 6.5 1.1 - - + -
66A LEU 4.1 1.2 + - - -
67A TRP* 1.3 70.9 - - - +
69A THR* 1.3 70.0 + - - +
202A MG 4.0 1.2 - - - -
----------------------------------------------------------
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