Contacts of the helix formed by residues 71 - 88 (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 THR 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.8 7.8 - - - +
68A ARG* 2.8 35.6 + - + +
69A ASP 3.9 2.7 - - - +
70A ASN* 1.3 82.1 - - - +
72A PRO* 1.3 76.1 - - + +
73A ASN* 3.8 3.2 + - - +
74A ALA* 2.9 25.0 + - - +
75A ILE* 3.1 15.4 + - - +
24B ASP* 3.5 41.3 + - + +
25B SER* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 6.4 1.6 - - - -
70A ASN 4.7 1.3 - - - +
71A THR* 1.3 88.3 - - + +
73A ASN* 1.3 61.9 + - - +
75A ILE* 3.7 8.7 + - + +
76A ALA* 3.0 26.9 + - - +
21B ARG* 5.0 13.9 - - - +
24B ASP* 6.4 0.2 - - + -
25B SER* 6.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 5.3 0.2 - - - +
21A ARG* 4.8 2.4 - - - +
22A LEU* 3.7 26.7 + - + +
25A SER* 3.5 15.7 + - - -
67A PHE* 3.5 29.7 - - + -
71A THR* 3.0 3.9 + - - +
72A PRO* 1.3 83.4 - - - +
74A ALA* 1.3 59.1 + - - +
76A ALA* 3.3 6.8 + - - +
77A ILE* 3.0 33.3 + - - +
25B SER* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.8 19.4 - - + +
68A ARG 3.3 27.1 - - - +
69A ASP* 4.6 2.7 - - - +
70A ASN 4.3 5.8 - - - +
71A THR* 2.9 12.8 + - - +
73A ASN* 1.3 79.5 - - - +
75A ILE* 1.3 59.8 + - + +
77A ILE* 3.3 5.7 + - - +
78A VAL* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 5.0 15.7 - - - +
71A THR 3.1 20.6 + - - +
72A PRO* 4.0 6.5 - - + +
74A ALA* 1.3 74.1 - - + +
76A ALA* 1.3 60.8 + - - +
77A ILE 3.1 0.2 - - - -
78A VAL* 3.2 12.5 + - + +
79A GLN* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 4.4 25.3 + - - +
21A ARG* 5.9 1.3 - - - +
22A LEU* 4.3 12.1 - - + -
72A PRO 3.0 20.1 + - - +
73A ASN* 3.4 11.4 - - - +
74A ALA 3.3 0.2 - - - -
75A ILE* 1.3 76.9 - - - +
77A ILE* 1.3 56.9 + - - +
79A GLN* 3.5 14.2 + - - +
80A LEU* 3.1 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.5 17.0 - - + -
61A MET* 4.2 13.9 - - + +
65A MET* 3.4 46.9 - - + +
67A PHE* 3.7 20.6 - - + -
73A ASN 3.0 19.5 + - - +
74A ALA* 3.5 8.7 - - - +
76A ALA* 1.3 75.6 - - - +
78A VAL* 1.3 64.9 + - + +
80A LEU* 3.2 13.0 + - + +
81A GLN* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 2.9 20.9 + - + +
75A ILE* 3.2 18.8 + - + +
77A ILE* 1.3 77.2 - - + +
79A GLN* 1.3 59.6 + - + +
81A GLN* 3.1 15.5 + - - +
82A GLU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 4.6 12.7 + - + +
18A SER* 5.2 6.9 + - - -
75A ILE* 2.9 38.2 + - + +
76A ALA* 3.7 13.6 - - - +
78A VAL* 1.3 79.3 - - + +
80A LEU* 1.3 57.6 - - + +
82A GLU* 3.1 19.0 + - - +
83A LEU* 2.9 28.1 + - - +
86A ARG* 4.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 3.9 37.7 - - + +
18A SER* 4.5 6.1 - - - +
19A LEU* 3.8 40.4 - - + -
22A LEU* 5.2 2.9 - - + -
61A MET* 3.8 17.1 - - - +
65A MET* 5.4 1.1 - - + -
76A ALA* 3.1 23.7 + - + +
77A ILE* 3.2 21.9 + - + +
79A GLN* 1.3 76.7 - - + +
81A GLN* 1.3 57.8 + - - +
83A LEU* 3.6 12.8 - - + +
84A SER* 3.0 28.4 + - - -
117A VAL* 5.8 0.4 - - + -
121A PHE* 4.4 10.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 5.1 1.9 + - - +
61A MET* 3.8 24.1 - - + +
62A GLU* 3.3 43.8 + - - +
77A ILE* 3.0 32.1 + - - +
78A VAL* 3.5 17.6 + - - +
79A GLN 3.1 0.2 - - - -
80A LEU* 1.3 77.1 - - - +
82A GLU* 1.3 63.1 + - - +
83A LEU 3.2 1.1 - - - -
84A SER* 3.4 3.3 + - - +
85A LEU* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 2.9 35.1 + - + +
79A GLN* 3.1 20.7 + - - +
81A GLN* 1.3 75.0 - - - +
83A LEU* 1.3 63.0 + - - +
85A LEU* 3.6 11.5 - - + +
86A ARG* 3.3 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 3.4 43.5 - - + +
11A ILE* 4.1 6.5 - - + -
15A HIS* 3.7 36.8 - - + +
79A GLN 2.9 15.8 + - - +
80A LEU* 3.6 7.9 - - + +
82A GLU* 1.3 75.3 - - - +
84A SER* 1.3 60.7 + - - +
86A ARG* 3.1 19.5 + - - +
87A LEU* 2.9 33.5 + - + +
121A PHE* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.8 5.2 - - - -
58A GLN* 3.0 44.5 + - - -
61A MET* 3.4 4.7 - - - +
80A LEU 3.0 17.4 + - - -
81A GLN 3.8 5.4 - - - -
82A GLU 3.4 0.4 - - - -
83A LEU* 1.3 75.5 - - - +
85A LEU* 1.3 66.1 + - - +
87A LEU* 3.0 19.6 + - - +
88A LYS* 3.0 20.8 + - - +
121A PHE* 3.8 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLN 3.1 13.4 + - - +
82A GLU* 3.6 14.6 - - - +
84A SER* 1.3 77.6 - - - +
86A ARG* 1.3 65.0 + - + +
88A LYS* 3.4 28.2 + - + +
89A SER 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.5 27.9 - - - +
10A MET* 3.7 31.9 + - - +
15A HIS* 4.8 7.9 + - - -
79A GLN 4.5 2.0 + - - -
82A GLU* 3.3 45.3 + - - +
83A LEU* 3.1 36.4 + - - +
85A LEU* 1.3 78.6 - - + +
87A LEU* 1.3 61.8 + - - +
88A LYS 3.3 0.2 + - - -
89A SER* 2.8 27.9 + - - -
90A CYS* 4.1 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 3.7 28.5 - - + -
11A ILE* 3.7 27.1 - - + -
54A PHE* 3.5 29.6 - - + -
83A LEU* 2.9 25.4 + - + +
84A SER* 3.0 9.6 + - - +
86A ARG* 1.3 75.3 - - - +
88A LYS* 1.3 59.4 + - - +
89A SER 3.1 0.2 - - - -
90A CYS* 2.8 29.1 + - - +
91A PHE* 3.1 21.4 - - + -
121A PHE* 4.3 6.1 - - + -
124A THR* 5.1 1.8 - - + -
128A LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 4.3 13.2 - - + -
55A LEU* 4.8 10.7 - - - +
58A GLN* 3.9 29.5 - - - +
84A SER* 3.0 19.5 + - - +
85A LEU* 3.5 22.9 - - + +
86A ARG 3.1 0.6 - - - -
87A LEU* 1.3 77.8 - - - +
89A SER* 1.3 56.9 + - - +
90A CYS 3.0 0.4 - - - -
91A PHE* 2.9 32.2 - - - +
----------------------------------------------------------
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