Contacts of the helix formed by residues 71 - 88 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ASP* 3.7 41.8 + - + -
25G SER* 5.9 0.4 - - - -
67H PHE* 4.0 2.9 - - - +
68H ARG* 2.7 35.2 + - + +
69H ASP 3.5 8.3 - - - +
70H ASN* 1.3 80.2 - - - +
72H PRO* 1.3 76.5 - - + +
73H ASN* 3.9 2.2 + - - -
74H ALA* 2.9 13.9 + - - +
75H ILE* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 5.8 3.4 - - + +
24G ASP* 5.5 4.0 - - + -
25G SER* 6.3 1.6 - - - -
70H ASN 4.5 1.8 - - - +
71H THR* 1.3 86.7 - - - +
73H ASN* 1.3 64.2 + - - +
75H ILE* 3.8 9.3 + - + +
76H ALA* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G SER* 2.8 41.0 + - - +
18H SER 4.7 1.7 - - - +
21H ARG* 4.5 2.9 - - - +
22H LEU* 3.5 30.4 + - + +
25H SER* 3.3 15.2 + - - -
26H GLN* 3.9 2.4 - - - +
67H PHE* 3.6 25.4 - - + -
71H THR* 3.1 3.4 + - - +
72H PRO* 1.3 82.7 - - - +
74H ALA* 1.3 65.4 + - - +
76H ALA* 3.5 5.1 - - - +
77H ILE* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H PHE* 3.6 23.6 - - + +
68H ARG 3.0 30.3 - - - +
69H ASP* 4.3 2.0 - - - -
70H ASN 4.2 5.2 - - - +
71H THR* 2.9 12.2 + - - +
73H ASN* 1.3 78.3 - - - +
75H ILE* 1.3 61.4 + - - +
77H ILE* 3.4 4.8 + - - +
78H VAL* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.8 11.7 - - - +
100A LYS* 3.6 18.6 - - - +
70H ASN* 3.5 35.4 - - - +
71H THR 2.9 17.1 + - - +
72H PRO* 4.0 7.6 - - + +
74H ALA* 1.3 71.9 - - - +
76H ALA* 1.3 66.6 + - - +
78H VAL* 3.3 9.0 + - + +
79H GLN* 3.1 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H HIS* 5.5 0.3 - - - -
18H SER* 4.0 33.2 + - - +
22H LEU* 4.8 6.7 - - + -
72H PRO 3.1 19.7 + - - +
73H ASN* 3.5 9.4 - - - +
74H ALA 3.2 0.4 - - - -
75H ILE* 1.3 77.4 - - - +
77H ILE* 1.3 62.2 + - + +
79H GLN* 3.1 12.7 + - - +
80H LEU* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU* 5.0 0.4 - - + -
22H LEU* 3.5 15.7 - - + -
61H MET* 4.1 23.3 - - + +
65H MET* 3.1 36.6 - - + +
67H PHE* 3.7 20.2 - - + -
73H ASN 3.0 17.4 + - - +
74H ALA* 3.8 5.2 - - - +
75H ILE 3.3 0.2 - - - -
76H ALA* 1.3 75.7 - - - +
78H VAL* 1.3 63.1 + - + +
80H LEU* 3.0 21.5 + - + +
81H GLN* 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.1 18.6 - - + +
86C ARG* 3.1 39.3 - - - +
88C LYS* 5.6 4.0 - - - +
74H ALA* 3.1 18.6 + - + +
75H ILE* 3.5 12.1 - - + +
77H ILE* 1.3 75.1 - - + +
79H GLN* 1.3 61.7 + - + +
81H GLN* 3.3 14.3 + - - +
82H GLU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H HIS* 4.2 25.9 + - + +
75H ILE* 3.1 38.9 + - + +
76H ALA* 3.1 10.8 + - - +
78H VAL* 1.3 78.5 - - + +
80H LEU* 1.3 58.1 + - - +
82H GLU* 3.8 6.9 - - - +
83H LEU* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H HIS* 3.9 33.7 - - + +
16H LEU* 5.6 1.3 - - + -
18H SER* 5.7 1.1 - - - +
19H LEU* 4.1 35.2 - - + -
22H LEU* 5.9 0.2 - - + -
61H MET* 3.6 13.7 - - - -
76H ALA* 3.0 19.7 + - + +
77H ILE* 3.0 22.5 + - + +
79H GLN* 1.3 75.5 - - - +
81H GLN* 1.3 55.5 + - - +
83H LEU* 3.6 15.2 - - + +
84H SER* 2.6 37.3 + - - -
117H VAL* 5.6 0.7 - - + -
121H PHE* 4.1 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.7 28.0 - - + +
88C LYS* 3.9 7.9 + - - +
58H GLN* 4.5 4.6 + - - +
61H MET* 3.7 26.6 + - + +
62H GLU* 3.3 43.9 + - - +
77H ILE* 2.9 38.5 + - - +
78H VAL* 3.7 9.8 - - - +
80H LEU* 1.3 75.6 - - - +
82H GLU* 1.3 62.5 + - - +
84H SER* 3.3 4.0 + - - -
85H LEU* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 4.8 1.6 - - - +
82C GLU* 2.6 42.9 - - - +
85C LEU* 3.8 9.0 - - + +
86C ARG* 2.7 34.2 + - - +
78H VAL 2.9 17.0 + - - +
79H GLN* 3.8 8.1 - - - +
81H GLN* 1.3 75.1 - - - +
83H LEU* 1.3 64.4 + - - +
84H SER 3.4 0.3 + - - -
85H LEU* 3.4 14.0 + - - +
86H ARG* 3.0 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H MET* 3.3 48.2 - - + +
11H ILE* 3.9 24.2 - - + +
15H HIS* 4.3 17.0 - - + +
79H GLN 2.8 19.3 + - - +
80H LEU* 3.6 28.3 - - + +
82H GLU* 1.3 78.4 - - - +
84H SER* 1.3 56.8 + - - +
86H ARG* 3.4 18.2 + - - +
87H LEU* 3.1 30.6 + - + +
121H PHE* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 3.7 12.2 - - - -
58H GLN* 2.9 44.7 + - - -
61H MET* 3.8 0.5 - - - +
80H LEU 2.6 21.4 + - - -
81H GLN 3.7 3.6 - - - -
82H GLU 3.2 0.6 - - - -
83H LEU* 1.3 76.0 - - - +
85H LEU* 1.3 63.8 + - - +
86H ARG 3.3 0.2 - - - -
87H LEU* 3.4 4.3 + - - +
88H LYS* 3.4 26.3 + - - +
121H PHE* 3.8 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 4.5 2.2 - - - +
78C VAL* 4.0 25.4 - - + +
81C GLN* 3.2 52.5 - - + +
82C GLU* 3.5 33.9 - - + +
85C LEU* 4.6 8.7 - - + -
81H GLN 3.2 18.1 + - - +
82H GLU* 3.7 8.7 - - - +
83H LEU 3.3 0.4 - - - -
84H SER* 1.3 80.0 - - - +
86H ARG* 1.3 60.2 + - + +
88H LYS* 3.6 34.4 + - - +
89H SER 4.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 5.9 4.9 - - - -
32B GLN* 4.1 27.6 + - - +
107B TYR* 6.6 0.2 - - + -
78C VAL* 6.2 2.0 - - + -
82C GLU* 5.1 5.2 - - - +
6H TYR* 3.9 9.6 + - + +
10H MET* 3.2 32.9 - - + +
82H GLU* 3.0 40.5 + - - +
83H LEU* 3.4 29.9 + - - +
85H LEU* 1.3 73.6 - - + +
87H LEU* 1.3 60.8 + - - +
88H LYS 3.1 3.7 + - - -
89H SER* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H CYS 4.5 0.9 - - - +
10H MET* 3.9 26.2 - - + +
11H ILE* 3.6 28.3 - - + -
54H PHE* 3.8 29.6 - - + -
83H LEU* 3.1 27.1 + - + +
84H SER* 3.7 9.0 - - - +
85H LEU 3.4 0.2 - - - -
86H ARG* 1.3 76.6 - - - +
88H LYS* 1.3 62.5 + - - +
89H SER 3.1 0.4 - - - -
90H CYS* 3.1 19.5 + - - +
91H PHE* 3.1 26.8 - - + -
121H PHE* 5.1 0.7 - - + -
124H THR* 4.9 0.9 - - + -
128H LEU* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C MET 5.7 0.8 + - - -
62C GLU* 3.9 22.8 + - - +
69C ASP* 4.2 10.9 - - - +
77C ILE* 5.7 1.0 - - - +
78C VAL* 4.9 7.9 - - - +
81C GLN* 3.4 24.0 + - - +
54H PHE* 4.5 11.2 - - + -
55H LEU* 5.1 9.9 - - + -
58H GLN* 6.2 1.3 - - + -
84H SER 3.4 9.8 + - - +
85H LEU* 3.6 33.5 - - - +
86H ARG 3.1 0.6 - - - -
87H LEU* 1.3 72.8 - - - +
89H SER* 1.3 57.3 + - - +
90H CYS 3.0 5.4 - - - -
91H PHE* 2.9 36.9 + - + +
93H LYS* 4.9 18.9 - - - +
----------------------------------------------------------
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