Contacts of the helix formed by residues 79 - 93 (chain H) in PDB entry 5U0A
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 79 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H GLY 3.9 1.0 + - - -
78H TRP* 1.3 75.5 - - - +
80H ALA* 1.3 65.4 + - - +
81H ASP* 3.1 32.9 + - - +
82H LEU* 3.1 20.3 + - + +
83H ALA* 2.7 27.8 + - - +
135H ARG* 4.4 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ARG* 3.8 35.9 + - - +
78H TRP 3.9 0.8 + - - -
79H ASP* 1.3 79.8 + - - +
81H ASP* 1.3 63.6 + - - +
83H ALA* 3.2 2.9 + - - +
84H ASP* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ASP* 3.1 14.9 + - - +
80H ALA* 1.3 83.2 - - - +
82H LEU* 1.3 59.3 + - + +
84H ASP* 3.4 6.2 + - - +
85H ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H TRP* 3.2 23.9 - - + -
79H ASP* 3.1 22.7 + - + +
81H ASP* 1.3 76.4 - - + +
83H ALA* 1.3 60.9 + - - +
85H ALA* 4.1 1.5 - - - +
86H GLY 2.9 23.2 + - - -
135H ARG* 4.4 27.8 - - + +
138H VAL* 4.4 4.9 - - + +
139H ALA* 4.1 34.3 - - + +
142H ALA* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ALA* 3.8 28.4 - - - +
73H LEU* 3.9 17.9 - - + +
74H ARG* 4.0 10.8 - - - +
78H TRP* 3.9 9.8 - - + -
79H ASP 2.7 21.8 + - - +
80H ALA* 3.6 8.5 - - - +
82H LEU* 1.3 75.6 - - - +
84H ASP* 1.3 56.8 + - - +
86H GLY* 3.4 0.7 + - - -
87H ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE* 4.4 2.1 - - - +
70H ALA* 4.7 8.4 - - + +
74H ARG* 5.7 1.8 - - - +
80H ALA 3.0 16.1 + - - +
81H ASP* 3.8 7.4 - - - +
82H LEU 3.3 0.2 - - - -
83H ALA* 1.3 77.0 - - - +
85H ALA* 1.3 56.8 + - - +
87H ALA* 3.4 4.0 + - - +
88H ARG* 3.0 52.1 + - - +
105H GLU* 5.8 0.2 - - - +
109H GLU 5.7 0.3 - - - -
110H ALA* 4.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ASP 3.0 18.2 + - - +
82H LEU* 4.1 3.8 - - - +
84H ASP* 1.3 76.1 - - - +
86H GLY* 1.3 57.5 + - - +
88H ARG* 3.3 11.5 + - - +
89H GLN* 2.9 36.3 + - + +
138H VAL* 4.2 4.5 - - + -
142H ALA* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 4.3 12.6 - - - -
78H TRP* 4.4 2.0 - - - -
82H LEU 2.9 18.6 + - - -
83H ALA 3.8 0.9 - - - -
85H ALA* 1.3 75.0 - - - +
87H ALA* 1.3 60.8 + - - +
89H GLN* 3.1 7.0 + - - +
90H VAL* 3.0 30.4 + - - +
131H ALA* 4.1 3.9 - - - +
138H VAL* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE* 3.4 40.1 - - + +
69H ILE* 3.9 19.4 - - + +
70H ALA* 4.2 2.9 - - + +
73H LEU* 4.2 1.2 - - - +
83H ALA 2.9 17.9 + - - +
84H ASP 4.0 1.3 - - - +
86H GLY* 1.3 71.7 - - - +
88H ARG* 1.3 66.9 + - - +
90H VAL* 3.0 21.6 + - - +
91H VAL* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE* 4.6 11.4 - - + -
84H ASP* 3.0 43.0 + - - +
85H ALA* 3.6 9.6 - - - +
87H ALA* 1.3 76.3 - - - +
89H GLN* 1.3 61.5 + - + +
91H VAL* 3.4 9.8 - - + +
92H LEU* 2.9 35.7 + - + +
102H LEU* 4.1 13.9 - - + +
105H GLU* 3.3 19.8 + - - +
111H PRO* 3.2 36.8 - - - +
147H PRO* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ALA* 2.9 26.4 + - + +
86H GLY* 3.1 10.3 + - - +
88H ARG* 1.3 78.8 - - - +
90H VAL* 1.3 64.1 + - - +
92H LEU* 4.1 7.0 - - - +
93H SER* 2.9 29.3 + - - -
138H VAL* 4.3 17.3 - - + -
141H GLU* 4.3 10.8 + - - +
142H ALA* 5.4 0.4 - - - +
147H PRO* 3.2 38.8 - - - +
148H LYS 2.7 26.1 + - - +
149H GLY* 3.9 1.6 - - - -
150H ILE* 3.8 9.1 + - + +
151H LEU* 3.3 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 5.9 0.4 - - + -
69H ILE* 3.9 28.5 - - + -
86H GLY 3.0 16.0 + - - +
87H ALA* 3.0 13.2 + - - +
89H GLN* 1.3 76.6 - - - +
91H VAL* 1.3 62.3 + - + +
93H SER* 3.1 7.8 + - - -
94H VAL* 3.1 26.0 - - - +
127H LEU* 4.4 25.1 - - + +
131H ALA* 3.5 25.4 - - + +
151H LEU* 4.4 4.9 - - + -
156H ILE* 3.9 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 4.0 19.5 - - + -
66H ILE* 3.7 39.9 - - + -
69H ILE* 5.7 1.1 - - + -
87H ALA 3.3 4.4 + - - +
88H ARG* 3.4 11.7 - - + +
90H VAL* 1.3 83.5 - - + +
92H LEU* 1.3 66.2 + - + +
93H SER 3.7 0.2 + - - -
94H VAL* 3.9 5.8 + - - +
99H GLY* 3.9 0.2 - - - -
100H ILE* 3.1 43.4 + - + +
102H LEU* 4.3 16.2 - - + -
113H THR* 4.5 5.8 - - + -
117H PHE* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ARG* 2.9 23.5 + - + +
89H GLN* 3.9 17.0 - - - +
90H VAL 3.3 0.4 - - - -
91H VAL* 1.3 79.9 - - + +
93H SER* 1.3 59.3 + - - +
94H VAL 3.3 1.5 + - - -
98H SER* 2.8 35.2 - - - +
99H GLY* 4.0 17.0 - - - +
100H ILE 5.5 2.9 - - - +
102H LEU* 6.1 4.0 - - + -
147H PRO* 3.1 35.4 - - + +
148H LYS* 4.5 1.8 - - - -
149H GLY* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H GLN 2.9 18.2 + - - -
90H VAL 3.1 10.7 + - - -
91H VAL 3.4 0.4 - - - -
92H LEU* 1.3 77.4 - - - +
94H VAL* 1.3 56.5 + - - +
149H GLY* 3.5 22.4 - - - +
151H LEU* 3.6 26.1 - - - +
153H ALA* 3.7 20.4 - - - +
156H ILE* 3.1 19.1 - - - +
----------------------------------------------------------
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