Contacts of the helix formed by residues 45 - 64 (chain A) in PDB entry 3UF2
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 ASP 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.4 2.7 - - + +
44A LYS* 1.3 76.0 - - - +
46A PRO* 1.3 66.3 - - - +
47A VAL* 4.0 3.4 + - - +
48A CYS* 3.0 30.5 + - + +
49A TYR* 2.8 35.9 + - - +
137A LYS* 2.7 32.4 + - - -
142A SER* 3.7 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS 3.2 10.5 - - - +
45A ASP* 1.3 92.3 - - - +
47A VAL* 1.3 64.8 + - + +
49A TYR* 3.4 8.8 - - + +
50A LEU* 3.2 30.4 + - + +
127A LEU* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 3.3 5.0 + - - +
46A PRO* 1.3 78.9 - - + +
48A CYS* 1.3 67.4 - - - +
50A LEU* 3.0 8.6 + - - +
51A LYS* 3.0 22.9 + - + +
127A LEU* 5.3 4.0 - - + -
134A ILE* 4.0 35.4 - - + +
135A PHE* 3.6 24.5 - - + -
137A LYS* 3.6 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.4 12.8 - - + +
45A ASP* 3.0 31.6 + - + +
47A VAL* 1.3 79.0 - - - +
49A TYR* 1.3 61.7 + - - +
51A LYS* 3.5 3.3 - - - +
52A LYS 3.2 17.8 + - - -
137A LYS* 3.9 8.3 - - - -
139A CYS* 2.0 60.6 - - + -
142A SER* 3.9 15.3 - - - -
143A PHE* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.6 22.2 - + - -
38A VAL* 3.8 32.8 + - + +
40A GLN* 3.3 48.2 + - + +
43A LEU* 3.6 25.5 - - - +
44A LYS 5.5 0.2 - - - -
45A ASP 2.8 19.2 + - - +
46A PRO* 3.4 9.4 - - + +
48A CYS* 1.3 78.0 - - - +
50A LEU* 1.3 78.2 + - + +
52A LYS* 4.0 0.5 - - - +
53A ALA* 3.0 34.0 + - + +
116A LYS* 5.6 1.6 - - - -
120A VAL* 5.3 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.2 14.8 + - + +
47A VAL 3.0 7.4 + - - +
49A TYR* 1.3 94.4 - - + +
51A LYS* 1.3 66.5 + - - +
53A ALA* 3.9 2.5 - - - +
54A PHE* 3.0 25.5 + - - +
91A PHE* 4.3 1.3 - - - -
119A ASN 5.0 0.2 - - - +
120A VAL* 4.5 16.7 - - + +
123A GLU* 3.7 36.1 - - + +
124A THR* 4.2 11.7 + - - +
127A LEU* 3.5 32.1 - - + -
135A PHE* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.0 15.2 + - + +
48A CYS* 3.5 8.5 - - - +
49A TYR 3.3 0.2 - - - -
50A LEU* 1.3 80.0 - - - +
52A LYS* 1.3 61.7 + - - +
54A PHE* 3.4 9.0 + - - +
55A LEU* 3.4 18.0 + - - +
91A PHE* 3.9 21.7 - - + -
92A THR* 3.0 21.1 + - - +
94A ASP* 3.0 27.2 + - - -
135A PHE* 3.4 39.5 + - + +
137A LYS* 2.9 23.9 + - + +
139A CYS* 3.5 21.3 - - - -
143A PHE* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 4.0 4.7 - - + -
43A LEU* 4.3 6.1 - - + -
48A CYS 3.2 12.0 + - - +
49A TYR 4.1 2.2 - - - +
51A LYS* 1.3 75.5 - - - +
53A ALA* 1.3 65.4 + - - +
54A PHE 3.1 1.3 - - - -
55A LEU* 3.0 21.8 + - + +
56A LEU* 3.0 36.5 + - + +
100A LYS* 5.0 2.6 - - - +
101A ALA* 3.0 40.2 + - - +
102A CYS* 4.0 14.4 - - + +
103A VAL* 4.3 11.2 - - + +
143A PHE* 4.1 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 9.1 - - + -
38A VAL* 3.4 20.5 - - + +
49A TYR* 3.0 26.1 + - + +
50A LEU* 3.9 6.5 - - - +
52A LYS* 1.3 76.6 - - - +
54A PHE* 1.3 57.1 + - - +
56A LEU* 3.3 3.4 + - - +
57A VAL* 2.8 36.3 + - - +
120A VAL* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 3.0 19.7 + - - +
51A LYS 3.4 4.9 - - - +
52A LYS 3.1 0.4 - - - -
53A ALA* 1.3 78.0 - - - +
55A LEU* 1.3 72.8 + - + +
57A VAL* 3.4 7.0 + - + +
58A GLN* 3.1 46.1 + - - +
84A SER* 3.8 15.5 - - - -
87A LEU* 3.5 44.2 - - + -
88A LYS* 4.3 22.2 - - + -
91A PHE* 3.8 39.0 - + + -
120A VAL* 4.2 16.8 - - + +
121A PHE* 4.7 7.9 - + - -
124A THR* 5.5 4.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
51A LYS 3.7 13.2 - - - +
52A LYS* 3.0 22.0 + - + +
54A PHE* 1.3 90.9 - - + +
56A LEU* 1.3 60.6 + - + +
58A GLN* 2.9 29.3 + - + +
59A ASP* 3.4 9.0 - - - +
88A LYS* 4.8 12.6 - - + +
91A PHE* 6.0 4.5 - - + -
93A LYS* 6.1 5.8 - - + +
143A PHE* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 4.0 20.8 - - + +
37A PHE* 3.7 13.9 - - + +
38A VAL* 3.3 44.6 - - + +
52A LYS* 3.0 25.6 + - + +
53A ALA 3.8 3.6 - - - +
55A LEU* 1.3 77.9 - - + +
57A VAL* 1.3 57.3 + - - +
59A ASP* 3.0 18.0 + - + +
60A ILE* 2.9 31.3 + - - +
100A LYS* 6.2 1.6 - - + -
103A VAL* 4.4 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.0 17.3 - - + -
53A ALA 2.8 25.1 + - - +
54A PHE* 3.5 8.7 - - + +
55A LEU 3.2 0.2 - - - -
56A LEU* 1.3 77.0 - - - +
58A GLN* 1.3 68.2 + - - +
60A ILE* 3.6 8.1 - - + +
61A MET* 2.9 37.7 + - + +
117A VAL* 4.3 20.0 - - + -
120A VAL* 4.2 20.2 - - + -
121A PHE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.1 37.0 + - + +
55A LEU* 2.9 15.7 + - + +
57A VAL* 1.3 81.5 - - - +
59A ASP* 1.3 63.2 + - - +
61A MET* 3.0 26.8 + - - +
62A GLU* 3.3 23.7 + - - +
81A GLN* 5.1 2.6 + - - +
84A SER* 3.0 35.0 + - - -
88A LYS* 3.9 23.3 + - - +
121A PHE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU 6.2 0.2 - - - +
55A LEU* 3.4 12.8 - - - +
56A LEU* 3.0 20.8 + - + +
58A GLN* 1.3 78.1 - - - +
60A ILE* 1.3 59.3 + - + +
62A GLU* 5.0 0.7 - - - -
63A ASP* 2.9 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.3 11.4 - - + -
36A GLU 3.9 14.1 - - - +
37A PHE* 3.7 32.3 - - + -
56A LEU 2.9 18.9 + - - +
57A VAL* 3.6 11.7 - - + +
58A GLN 3.2 0.2 - - - -
59A ASP* 1.3 76.1 - - + +
61A MET* 1.3 61.5 + - - +
64A THR* 3.0 15.1 + - - +
65A MET* 2.9 50.4 + - + -
113A LEU* 4.1 33.4 - - + -
117A VAL* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.9 27.9 + - + +
58A GLN* 3.0 37.9 - - - +
60A ILE* 1.3 77.9 - - - +
62A GLU* 1.3 62.4 + - - +
65A MET* 3.0 47.9 - - + +
66A ARG* 4.9 0.2 - - - +
77A ILE* 4.2 11.8 - - + +
80A LEU* 3.8 31.0 - - - +
81A GLN* 3.8 30.3 - - + +
84A SER* 3.4 15.3 - - - +
117A VAL* 5.2 1.6 - - + -
121A PHE* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN 3.3 14.8 + - - +
59A ASP* 4.7 0.9 - - - -
60A ILE 3.3 0.2 - - - -
61A MET* 1.3 81.8 - - - +
63A ASP* 1.3 75.3 + - - +
66A ARG* 3.6 17.3 - - - +
81A GLN* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 2.9 27.9 + - + +
62A GLU* 1.3 97.5 - - - +
64A THR* 1.3 63.9 + - - +
66A ARG* 3.7 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.9 17.0 - - + -
34A THR 4.6 7.5 + - - +
35A PHE* 4.5 11.5 - - + +
60A ILE* 3.0 23.0 + - - +
63A ASP* 1.3 82.8 - - - +
65A MET* 1.3 62.1 + - + +
66A ARG* 3.0 8.7 + - - +
113A LEU* 3.8 25.1 - - + -
27B MET* 5.3 0.7 - - + -
28B GLU 3.5 16.3 - - - +
29B THR* 4.2 12.3 - - + +
----------------------------------------------------------
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