Contacts of the helix formed by residues 65 - 74 (chain B) in PDB entry 2FA5
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 SER 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.7 1.0 + - - -
64B SER* 1.3 74.3 - - - +
66B ALA* 1.3 64.4 + - - +
67B SER* 3.6 8.7 + - - -
68B GLU* 3.0 39.7 + - - +
69B VAL* 3.1 25.4 + - - +
105B SER* 3.2 24.0 - - - -
106B MSE 6.1 0.7 - - - -
107B LEU* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 1.3 73.1 - - - +
67B SER* 1.3 62.5 + - - +
69B VAL* 3.2 10.3 + - - +
70B SER* 3.1 26.5 + - - -
80B VAL* 3.8 7.4 - - + +
81B SER* 4.9 12.3 - - - +
84B VAL* 4.2 23.8 - - + -
105B SER 4.3 2.8 + - - +
107B LEU* 3.9 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 3.1 10.4 + - - -
66B ALA* 1.3 79.8 - - - +
68B GLU* 1.3 57.2 + - - +
70B SER* 3.4 5.1 + - - -
71B ASP* 3.0 26.9 + - - +
77B LYS* 3.8 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 4.5 1.2 - - - +
64B SER* 3.5 16.0 + - - +
65B SER* 3.0 39.1 + - - +
67B SER* 1.3 75.3 - - - +
69B VAL* 1.3 65.8 + - - +
71B ASP* 3.5 7.8 - - - +
72B ARG* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 5.6 0.7 - - + -
54B VAL* 4.3 22.4 - - + +
57B ILE* 4.0 26.7 - - + -
58B LEU* 4.5 9.0 - - + -
64B SER* 4.3 9.2 - - - -
65B SER 3.1 17.3 + - - +
66B ALA* 3.2 10.1 + - - +
68B GLU* 1.3 77.2 - - - +
70B SER* 1.3 60.5 + - - +
72B ARG* 3.5 7.1 - - - +
73B THR* 2.8 39.4 + - + +
75B MSE 5.5 2.7 - - - -
80B VAL* 3.8 21.8 - - + -
84B VAL* 5.8 0.7 - - + -
107B LEU* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA 3.1 10.3 + - - -
67B SER* 3.6 9.5 - - - -
68B GLU 3.3 0.2 - - - -
69B VAL* 1.3 73.6 - - - +
71B ASP* 1.3 57.5 + - - +
73B THR* 3.9 4.3 - - - -
74B ALA* 2.8 34.5 + - - -
75B MSE 3.3 16.1 + - - +
77B LYS* 3.6 26.8 + - - +
80B VAL* 3.2 30.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 6.1 0.7 - - - -
67B SER* 3.0 15.2 + - - +
68B GLU* 3.5 12.6 - - - +
70B SER* 1.3 79.9 - - - +
72B ARG* 1.3 69.1 + - - +
74B ALA* 3.3 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 4.1 4.8 + - - -
24A TYR* 3.7 19.0 + - - +
25A ARG* 5.7 0.3 + - - -
28A VAL* 3.5 19.2 - - - +
57B ILE* 4.1 23.1 - - + +
61B TYR* 3.0 58.1 + - - +
64B SER* 4.5 6.0 + - - -
68B GLU* 3.0 28.8 + - - +
69B VAL* 3.5 7.6 - - - +
71B ASP* 1.3 85.6 - - - +
73B THR* 1.3 64.6 + - + +
74B ALA* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.7 27.4 - - + +
28A VAL* 4.1 14.3 - - - +
31A ASN* 3.0 23.4 + - - +
53B ARG* 4.2 17.9 - - + -
57B ILE* 4.2 7.9 - - + -
69B VAL* 2.8 25.3 + - + +
70B SER 3.5 0.5 + - - -
72B ARG* 1.3 79.6 - - + +
74B ALA* 1.3 66.3 + - - +
75B MSE 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.2 1.6 - - + +
31A ASN* 3.4 32.4 - - + +
32A ARG* 3.7 28.9 - - + +
70B SER 2.8 11.4 + - - -
71B ASP 3.3 8.6 + - - +
72B ARG 3.5 0.2 - - - -
73B THR* 1.3 80.8 - - - +
75B MSE 1.3 62.1 + - - +
----------------------------------------------------------
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