Contacts of the helix formed by residues 51 - 62 (chain A) in PDB entry 1OFD
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 PRO 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 3.3 6.0 - - - +
50A ILE* 1.3 86.2 - - + +
52A ARG* 1.3 64.5 + - - +
53A GLU* 3.3 2.7 - - - -
54A LEU* 3.2 17.6 + - + -
55A LEU* 3.1 31.1 + - + +
130A GLN* 6.0 0.4 - - - +
173A ILE* 4.0 17.9 - - + -
175A TYR* 4.7 6.1 - - + +
195A GLY 5.5 0.2 - - - -
196A TYR* 3.8 46.2 - - + +
197A THR* 4.2 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 2.9 19.3 + - + +
51A PRO* 1.3 70.8 - - - +
53A GLU* 1.3 58.5 + - - +
55A LEU* 3.3 6.9 + - - +
56A ALA* 2.9 29.3 + - - +
66A MET* 4.0 39.0 + - + +
67A PRO 2.7 34.1 + - - -
68A ASP* 3.5 6.8 + - - +
69A GLY* 3.3 29.1 - - - +
72A LEU* 4.6 10.7 - - + +
197A THR* 5.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO 3.3 0.6 - - - -
52A ARG* 1.3 76.9 - - - +
54A LEU* 1.3 63.3 + - - +
56A ALA* 3.5 17.3 - - + +
57A GLN* 4.1 8.7 + - - +
194A PRO 5.2 0.2 - - - +
195A GLY* 3.5 30.5 - - - +
197A THR* 4.1 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 3.2 21.9 + - + +
53A GLU* 1.3 79.1 - - - +
55A LEU* 1.3 63.4 + - + +
57A GLN* 3.3 36.4 + - - +
58A TRP 4.2 1.0 + - - -
108A ARG* 4.1 18.3 + - - +
175A TYR* 4.6 0.7 - - - +
190A ASP* 3.4 41.5 - - + +
193A ASN* 3.3 38.1 - - + +
195A GLY* 3.9 13.1 + - - +
196A TYR* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.7 30.7 - - + -
51A PRO* 3.1 22.4 + - + +
52A ARG* 3.3 5.6 + - - +
54A LEU* 1.3 73.9 - - + +
56A ALA* 1.3 64.7 + - - +
58A TRP* 3.1 16.9 + - - +
59A PHE* 3.3 26.0 + - + -
66A MET* 4.6 1.6 - - - -
72A LEU* 4.4 8.1 - - + -
74A VAL* 3.8 22.4 - - + -
108A ARG* 3.5 33.2 - - - +
130A GLN* 3.8 11.9 - - - +
132A LEU* 4.3 16.4 - - + -
173A ILE* 6.0 0.4 - - + -
175A TYR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG 2.9 11.3 + - - +
53A GLU* 3.5 15.9 - - - +
54A LEU 3.2 0.4 - - - -
55A LEU* 1.3 75.7 - - - +
57A GLN* 1.3 56.7 + - + +
59A PHE* 3.3 4.1 + - - +
60A ASN* 2.9 35.9 + - - +
66A MET* 3.5 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 4.1 8.5 - - - +
54A LEU* 3.5 32.4 - - - +
55A LEU 3.1 0.8 - - - -
56A ALA* 1.3 76.6 - - + +
58A TRP* 1.3 57.1 + - - +
60A ASN* 3.5 7.6 - - - +
61A THR* 3.0 34.5 + - - +
193A ASN* 4.4 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 4.2 0.6 + - - -
55A LEU* 3.1 13.3 + - - +
57A GLN* 1.3 80.5 - - - +
59A PHE* 1.3 81.7 + + - +
61A THR* 4.6 0.9 - - - -
62A ARG* 3.1 80.3 + - - +
64A LEU* 4.0 17.5 - - + -
105A LEU* 3.8 22.7 - - + -
106A GLY* 3.8 6.5 - - - -
107A TRP 3.0 38.4 + - - -
108A ARG* 3.6 36.9 - - + +
132A LEU* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.3 25.2 + - + -
56A ALA 3.3 8.1 + - - +
58A TRP* 1.3 100.7 - + - +
60A ASN* 1.3 61.9 + - - +
62A ARG 3.3 1.7 + - - -
63A ASN 3.1 3.3 + - - -
64A LEU* 2.9 49.4 + - + +
65A PRO 3.4 28.0 - - - -
66A MET* 3.6 28.5 - - + -
67A PRO* 3.7 8.3 - - + -
72A LEU* 3.8 35.0 - - + -
105A LEU* 3.7 20.9 - - + -
132A LEU* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 2.9 23.1 + - - +
57A GLN* 3.5 9.0 - - - +
59A PHE* 1.3 74.5 - - - +
61A THR* 1.3 66.0 + - - +
63A ASN* 3.1 14.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
57A GLN* 3.0 18.4 + - - +
58A TRP* 3.8 5.4 - - - -
60A ASN* 1.3 76.5 - - - +
62A ARG* 1.3 78.2 + - + +
63A ASN* 3.6 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TRP* 3.1 84.6 + - - +
59A PHE* 3.3 4.8 + - - +
60A ASN 3.1 0.8 - - - -
61A THR* 1.3 99.7 - - + +
63A ASN* 1.3 69.0 + - - +
64A LEU* 3.2 24.3 + - + +
107A TRP 4.4 5.1 + - - -
108A ARG* 5.7 0.4 - - - +
----------------------------------------------------------
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