Contacts of the helix formed by residues 91 - 110 (chain B) in PDB entry 5PNZ
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 ASN 91 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.9 13.2 - - - -
39B LEU* 4.6 0.4 - - - +
89B TYR* 3.4 7.9 - - - +
90B LYS* 1.3 87.8 - - - +
92B LEU* 1.3 63.1 + - - +
93B HIS* 3.2 11.8 + - - +
94B GLU* 3.0 50.0 + - - +
95B PHE* 3.6 7.1 + - - +
144B GLU* 4.2 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.2 6.5 - - + +
38B LEU* 5.5 0.7 - - + -
39B LEU* 3.6 29.4 - - + -
91B ASN* 1.3 75.2 - - - +
93B HIS* 1.3 64.8 + - - +
95B PHE* 3.1 4.3 + - + +
96B GLU* 2.9 31.1 + - + +
131B LEU* 4.1 27.1 - - + +
134B ALA* 3.8 14.4 - - + -
135B ARG* 3.6 56.8 - - + +
138B VAL* 3.9 20.2 - - + -
144B GLU* 4.4 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 3.2 12.0 + - - +
92B LEU* 1.3 79.0 - - - +
94B GLU* 1.3 59.0 + - - +
96B GLU* 3.1 23.6 + - + +
97B GLU* 2.9 65.2 + - + +
135B ARG* 3.9 8.9 - - - +
144B GLU* 5.1 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 3.2 30.0 + - - +
88B GLY 3.6 3.1 - - - +
89B TYR* 3.6 13.0 - - + -
90B LYS* 2.9 38.5 + - - +
91B ASN* 3.0 28.1 + - - +
92B LEU 3.3 0.2 - - - -
93B HIS* 1.3 75.9 - - - +
95B PHE* 1.3 61.6 + - - +
97B GLU* 3.4 18.5 + - - +
98B ASP* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 43.1 - - + -
42B VAL* 3.6 32.1 - - + -
43B LEU* 4.0 29.4 - - + -
46B LEU* 4.2 9.0 - - + -
80B MET* 3.5 29.4 - - + +
84B LEU* 4.9 2.0 - - + -
89B TYR* 3.6 33.5 - + + -
91B ASN 3.6 1.0 + - - -
92B LEU* 3.1 9.9 + - + +
94B GLU* 1.3 75.9 - - - +
96B GLU* 1.3 68.4 + - - +
98B ASP 3.1 3.3 + - - -
99B PHE* 3.1 19.7 + - + -
131B LEU* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 2.9 27.2 + - + +
93B HIS* 3.3 34.7 - - + +
95B PHE* 1.3 79.7 - - - +
97B GLU* 1.3 57.6 + - - +
99B PHE* 3.2 7.6 + - - +
100B ASP* 2.9 38.7 + - - +
131B LEU* 3.9 43.7 - - + +
135B ARG* 3.5 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 2.9 48.9 + - + +
94B GLU* 3.6 22.7 - - - +
95B PHE 3.2 0.2 - - - -
96B GLU* 1.3 76.6 - - + +
98B ASP* 1.3 62.8 + - - +
100B ASP* 3.4 10.5 + - - +
101B LEU* 3.1 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B MET* 3.4 37.1 - - + +
80B MET* 3.8 11.6 - - + -
83B ARG* 3.1 29.9 + - - +
89B TYR* 2.6 30.8 + - - +
94B GLU 3.3 3.0 + - - +
95B PHE 3.1 8.2 + - - +
97B GLU* 1.3 77.2 - - - +
99B PHE* 1.3 65.3 + - - +
101B LEU* 3.1 22.9 + - - +
102B ILE* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.7 27.6 - - + -
77B PHE* 4.2 23.6 - + - -
80B MET* 3.9 12.2 - - + -
95B PHE* 3.1 13.8 + - + +
96B GLU* 3.2 9.8 + - - +
98B ASP* 1.3 76.8 - - - +
100B ASP* 1.3 73.0 + - - +
102B ILE* 3.1 18.2 + - + +
103B ILE* 3.2 40.7 + - + +
123B LEU* 3.5 29.6 - - + -
124B ARG* 4.5 6.3 - - + -
127B GLY* 4.0 18.8 - - - -
128B GLY* 4.7 0.9 - - - -
131B LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 2.9 25.3 + - - +
97B GLU* 3.7 8.9 - - - +
99B PHE* 1.3 88.0 - - - +
101B LEU* 1.3 52.2 + - - +
103B ILE* 3.7 5.8 - - - +
104B ASP* 2.7 51.6 + - - +
131B LEU* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.6 43.3 - - + +
75B MET* 3.8 20.6 - - + -
97B GLU 3.1 13.5 + - - +
98B ASP* 3.1 24.9 + - - +
100B ASP* 1.3 72.9 - - - +
102B ILE* 1.3 61.1 + - - +
104B ASP* 4.6 4.7 - - + -
105B ASN* 2.8 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.4 35.8 - - + +
75B MET* 3.7 28.9 - - + +
76B ASP* 3.6 25.6 - - - -
77B PHE* 3.6 29.6 - - + +
80B MET* 3.7 15.0 - - - -
98B ASP 3.2 10.0 + - - +
99B PHE* 3.1 10.7 + - + +
101B LEU* 1.3 80.5 - - - +
103B ILE* 1.3 68.2 + - + +
105B ASN* 4.1 3.1 - - - +
106B CYS* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 5.1 1.1 - - + -
99B PHE* 3.2 46.5 + - + +
100B ASP* 3.8 8.3 - - - +
102B ILE* 1.3 78.8 - - + +
104B ASP* 1.3 72.1 + - - +
106B CYS* 3.3 3.3 + - - +
107B MET* 3.0 41.7 + - - +
120B ALA* 3.6 29.1 - - + +
123B LEU* 3.9 17.5 - - + -
124B ARG* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.2 36.3 + - - +
100B ASP* 2.7 35.0 + - - +
101B LEU* 4.2 5.7 - - + +
103B ILE* 1.3 83.1 - - - +
105B ASN* 1.3 59.6 + - - +
107B MET* 3.3 1.7 + - - +
108B LYS* 2.9 31.8 + - - +
124B ARG* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.6 17.6 + - - +
71B ILE* 3.4 31.9 - - + +
72B LYS 5.5 0.2 + - - -
73B HIS 2.8 27.1 + - - +
74B PRO* 3.7 8.9 - - - +
75B MET 3.8 7.8 + - - +
101B LEU* 2.8 37.6 + - - +
102B ILE* 4.1 3.8 - - - +
104B ASP* 1.3 77.3 - - - +
106B CYS* 1.3 57.7 + - - +
108B LYS* 3.4 2.3 + - - +
109B TYR* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 5.3 2.5 - - - -
55B PHE* 3.8 24.9 - - + -
67B TYR* 5.3 0.4 - - - -
102B ILE 3.3 14.8 + - - +
103B ILE 3.3 4.4 + - - +
104B ASP 3.2 0.4 - - - -
105B ASN* 1.3 81.2 - - - +
107B MET* 1.3 56.1 + - - +
109B TYR* 4.9 0.2 - - - -
110B ASN* 3.0 51.2 + - - +
117B TYR* 4.5 13.4 - - - -
119B ALA* 5.9 0.9 - - - -
120B ALA* 3.8 18.6 - - + -
202B EDO 3.8 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS 3.6 21.8 - - - +
71A ILE* 5.2 1.1 - - + -
108A LYS* 3.3 35.1 - - + +
103B ILE* 3.0 35.2 + - - +
104B ASP* 3.3 2.2 + - - +
106B CYS* 1.3 76.6 - - - +
108B LYS* 1.3 55.1 + - - +
110B ASN 3.2 1.8 - - - +
117B TYR* 3.3 44.5 - - + +
120B ALA* 3.8 14.8 - - + -
121B VAL* 3.9 14.8 - - + -
124B ARG* 3.8 17.0 - - - +
201B NA 2.3 31.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 3.6 57.4 - - + +
108A LYS* 3.9 10.0 - - + +
110A ASN 5.4 0.3 - - - +
111A ALA* 6.2 0.2 - - - -
112A ARG* 4.4 4.5 + - - +
117A TYR* 3.6 19.8 + - - +
124A ARG* 4.1 11.9 - - - +
70B HIS* 2.9 31.1 + - + +
71B ILE* 3.8 14.1 - - + +
72B LYS* 4.8 6.7 - - - +
104B ASP 2.9 18.0 + - - +
105B ASN* 3.8 4.5 - - - +
107B MET* 1.3 79.0 - - - +
109B TYR* 1.3 63.6 + - - +
110B ASN 4.3 0.3 - - - +
201B NA 3.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 2.9 52.5 + - - +
64B VAL* 3.2 22.3 - - + +
66B ASP* 2.5 32.9 + - - -
67B TYR* 3.8 30.5 - + + -
70B HIS* 4.1 20.9 - + + -
71B ILE* 4.3 4.5 - - + -
105B ASN 2.9 17.8 + - - +
106B CYS* 4.9 0.4 - - - -
108B LYS* 1.3 79.5 - - - +
110B ASN* 1.3 75.7 + - - +
111B ALA 4.1 0.3 + - - -
202B EDO 3.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 6.2 0.2 - - - -
106B CYS* 3.0 27.3 + - - +
107B MET 3.2 3.5 - - - +
108B LYS 4.7 0.2 - - - -
109B TYR* 1.3 93.9 - - - +
111B ALA* 1.3 58.1 + - - +
114B THR* 3.7 20.0 + - - +
117B TYR* 3.5 12.6 - - + +
201B NA 2.3 29.6 - - - -
202B EDO 3.2 30.9 + - - -
----------------------------------------------------------
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