Contacts of the helix formed by residues 53 - 71 (chain A) in PDB entry 2W99
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 LEU 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.7 8.5 - - + +
50A LYS 4.7 6.1 - - - +
51A GLU 3.5 13.2 + - - +
52A VAL* 1.3 87.1 - - - +
54A PRO* 1.3 71.6 - - + +
55A SER* 4.3 9.9 - - - +
56A MET* 2.8 48.7 + - + +
57A ARG 3.3 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.6 38.1 - - + -
53A LEU* 1.3 93.4 - - + +
55A SER* 1.3 55.7 + - - +
57A ARG* 3.5 4.6 + - + +
58A LYS* 2.9 27.2 + - - +
193A VAL* 4.0 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 2.8 10.4 + - - +
54A PRO* 1.3 78.3 - - - +
56A MET* 1.3 73.9 + - - +
58A LYS* 3.2 14.8 - - - +
59A ILE* 3.2 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU 3.5 19.1 - - - +
52A VAL* 4.0 2.2 - - + -
53A LEU* 2.8 44.1 + - + +
55A SER* 1.3 81.9 - - - +
57A ARG* 1.3 57.3 + - - +
59A ILE* 2.9 25.7 + - + +
60A VAL* 2.8 23.4 + - - +
96A LYS* 3.8 43.5 - - + +
99A LEU* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.6 16.1 + - - +
45A PHE* 4.1 14.6 - - + -
52A VAL* 5.0 3.8 - - + +
53A LEU 3.3 7.6 + - - +
54A PRO* 3.7 10.3 - - + +
56A MET* 1.3 74.7 - - - +
58A LYS* 1.3 60.7 + - - +
60A VAL* 3.9 8.3 - - - -
61A ALA* 2.9 34.9 + - - +
82A MET* 3.5 13.5 - - + +
85A LEU* 4.0 17.7 - - + -
86A ASP* 2.9 36.6 + - - -
89A LEU* 5.5 2.2 - - + -
99A LEU* 3.9 4.8 - - + +
190A ALA 2.9 28.6 + - - -
191A THR* 3.5 10.3 + - - +
192A ASP 3.1 30.8 + - - -
193A VAL* 4.2 4.2 - - - +
195A PHE* 3.8 9.5 - - - +
196A ILE* 3.9 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO 2.9 14.9 + - - +
55A SER* 3.2 16.4 - - - +
57A ARG* 1.3 76.4 - - - +
59A ILE* 1.3 60.4 + - + +
61A ALA* 4.0 0.4 - - - +
62A THR* 2.8 52.9 + - + +
191A THR* 2.9 40.8 + - - +
192A ASP* 5.1 5.4 - - - +
261A GLN* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.2 21.3 - - - +
56A MET* 2.9 14.6 + - + +
58A LYS* 1.3 79.4 - - + +
60A VAL* 1.3 61.8 + - + +
62A THR* 3.3 6.6 + - - +
63A TRP* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET 2.8 18.6 - - - +
57A ARG* 3.9 4.5 - - - +
59A ILE* 1.3 76.3 - - + +
61A ALA* 1.3 59.7 + - - +
63A TRP* 3.3 13.6 + - + +
64A MET* 2.8 38.8 + - - +
85A LEU* 4.8 6.5 - - + -
99A LEU* 3.0 34.1 - - + +
100A GLN* 3.8 28.7 - - + +
103A GLY* 4.0 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.9 16.2 + - - +
58A LYS 4.0 0.9 - - - +
60A VAL* 1.3 76.5 - - - +
62A THR* 1.3 57.9 + - - +
64A MET* 3.1 1.6 + - - -
65A LEU 2.9 23.6 + - - -
78A PHE* 3.1 12.4 - - + -
82A MET* 3.1 43.2 - - + +
191A THR* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 2.8 42.1 + - + +
59A ILE* 3.3 9.0 + - - +
61A ALA* 1.3 72.3 - - - +
63A TRP* 1.3 66.0 + - - +
65A LEU* 3.4 7.2 + - + +
66A GLU* 3.2 33.6 + - - +
191A THR* 3.6 27.4 - - + +
261A GLN* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.0 22.3 + - + +
60A VAL* 3.4 14.1 - - + +
62A THR* 1.3 75.1 + - - +
64A MET* 1.3 82.4 + - + +
66A GLU* 3.4 15.2 + - + +
67A VAL* 3.2 30.6 + - + +
100A GLN* 4.0 25.6 + - + -
103A GLY 4.3 0.2 - - - -
104A ALA* 3.8 24.5 - - + -
107A MET* 3.6 28.0 - - + -
124A LEU* 4.6 4.7 - - + -
127A TYR* 3.2 37.9 + - + -
128A THR* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 2.8 26.9 + - - +
61A ALA 3.4 6.5 - - - +
63A TRP* 1.3 88.6 - - + +
65A LEU* 1.3 62.4 + - - +
67A VAL* 3.2 4.3 + - - +
68A CYS* 3.0 27.7 + - - -
78A PHE* 3.8 9.2 - - + -
81A ALA* 3.3 38.1 - - + +
82A MET* 3.6 30.5 - - + +
85A LEU* 4.4 5.2 - - + -
103A GLY* 3.6 28.5 - - - +
106A CYS* 4.4 1.1 - - + -
107A MET* 3.7 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA 2.9 12.2 + - - +
62A THR* 3.6 12.1 - - + +
64A MET* 1.3 79.1 - - - +
66A GLU* 1.3 57.2 + - + +
68A CYS* 3.4 4.4 + - + +
69A GLU* 2.9 52.8 + - + +
78A PHE* 3.7 32.3 - - + -
187A ALA* 4.1 24.0 - - + +
191A THR* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 3.2 21.0 + - - +
63A TRP* 3.7 15.7 - - + +
64A MET 3.3 0.2 - - - -
65A LEU* 1.3 75.0 - - + +
67A VAL* 1.3 56.7 + - + +
69A GLU* 3.7 12.9 - - - +
70A GLU* 2.6 39.7 + - - +
127A TYR* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TRP* 3.2 31.6 + - + +
64A MET 3.2 8.8 + - - +
66A GLU* 1.3 77.8 - - + +
68A CYS* 1.3 53.5 - - - +
70A GLU* 4.4 4.3 - - - -
71A GLN* 2.7 45.5 + - + +
107A MET* 4.1 20.4 - - + -
119A LEU* 4.7 8.3 - - + -
124A LEU* 4.5 7.4 - - + -
127A TYR* 3.7 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET 3.0 20.8 + - - +
65A LEU* 3.7 7.4 - - + +
67A VAL* 1.3 74.0 - - - +
69A GLU* 1.3 61.6 + - + +
72A LYS* 3.2 1.9 + - - -
73A CYS* 2.7 47.9 + - + +
74A GLU 5.7 0.7 - - - +
75A GLU* 6.4 1.8 - - - -
77A VAL* 4.4 9.9 - - + -
78A PHE* 3.8 38.1 - - + +
107A MET* 3.9 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 2.9 46.4 + - + +
66A GLU* 3.7 13.5 - - - +
68A CYS* 1.3 74.8 - - + +
70A GLU* 1.3 66.8 + - - +
72A LYS* 2.9 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU 2.6 23.5 + - - +
67A VAL 3.9 0.7 - - - +
69A GLU* 1.3 73.3 - - - +
71A GLN* 1.3 62.6 + - - +
72A LYS* 3.4 12.0 + - - +
127A TYR* 3.2 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 2.7 22.6 + - + +
70A GLU* 1.3 75.9 + - - +
72A LYS* 1.3 70.6 + - - +
73A CYS* 3.0 19.3 + - - -
119A LEU* 4.0 16.6 - - + +
123A LYS* 3.5 25.2 - - - +
127A TYR* 2.3 48.6 + - + +
----------------------------------------------------------
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