Contacts of the helix formed by residues 108 - 126 (chain B) in PDB entry 3SDI
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 PRO 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TYR* 3.5 24.7 - - + +
106B ASP 3.4 8.3 - - - +
107B ILE* 1.3 89.4 - - + +
109B VAL* 1.3 67.9 + - - +
110B GLU* 4.7 3.1 - - + +
111B ILE* 3.2 34.2 + - + +
112B LEU* 3.4 8.0 + - - +
142B ASP* 3.5 19.7 - - + +
144B ARG* 5.9 8.3 - - + -
66J TYR* 4.5 1.8 - - - +
70J GLU* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.9 29.8 - - + -
107B ILE 3.4 0.8 + - - +
108B PRO* 1.3 69.7 - - - +
110B GLU* 1.3 63.4 + - - +
112B LEU* 3.2 4.3 + - - +
113B VAL* 3.0 26.3 + - + +
138B TYR* 4.9 3.8 - - + -
140B GLY* 3.8 35.7 - - - +
141B TYR 3.8 8.1 - - - +
142B ASP* 2.9 15.2 + - + +
147B GLN* 3.7 20.4 - - + +
149B TYR* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 3.3 2.9 - - + +
109B VAL* 1.3 76.7 - - - +
111B ILE* 1.3 56.2 + - + +
113B VAL* 3.1 4.6 + - - +
114B ARG* 2.7 54.2 + - - +
142B ASP* 4.7 0.2 + - - -
144B TYR* 4.7 18.3 + - - +
147B GLN* 4.2 5.5 + - - +
149B TYR* 3.7 23.8 + - + +
157B TYR* 3.0 34.1 + - + +
62C ILE* 4.3 14.9 - - - +
64C PRO* 5.0 6.8 - - - +
70J GLU* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 4.3 8.5 - - + +
99B TYR* 4.1 9.9 - - + -
107B ILE* 3.7 17.7 - - + -
108B PRO* 3.2 32.5 + - + +
110B GLU* 1.3 76.8 - - + +
112B LEU* 1.3 63.3 - - - +
114B ARG* 3.4 16.3 + - - +
115B ARG* 3.2 22.7 + - - +
66J TYR* 3.3 27.6 - - + +
69J ARG* 6.4 0.2 - - - -
70J GLU* 3.4 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.6 35.0 - - + -
71B ASN* 5.5 0.7 - - + -
74B ILE* 3.9 25.4 - - + -
92B ALA* 4.2 28.0 - - + +
95B HIS* 4.4 7.4 - - + -
96B ALA* 4.3 6.7 - - + -
107B ILE* 3.8 30.3 - - + +
108B PRO 3.4 3.7 + - - +
109B VAL 3.2 8.8 + - - +
111B ILE* 1.3 80.3 - - - +
113B VAL* 1.3 68.6 + - + +
115B ARG* 3.4 2.9 + - - +
116B LEU* 3.3 19.4 + - + +
138B TYR* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 6.1 0.2 - - + -
109B VAL* 3.0 17.9 + - + +
110B GLU* 3.6 8.1 - - - +
112B LEU* 1.3 78.4 - - + +
114B ARG* 1.3 61.9 + - - +
116B LEU* 3.4 2.8 + - - +
117B SER* 3.0 28.2 + - - +
138B TYR* 3.4 57.8 + - + -
149B TYR* 4.0 17.9 - - + -
157B TYR* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 2.7 42.1 + - - +
111B ILE* 3.8 19.2 + - - +
112B LEU 3.3 0.2 - - - -
113B VAL* 1.3 72.8 - - - +
115B ARG* 1.3 56.3 + - - +
117B SER* 3.5 2.1 + - - -
118B ASP* 3.0 41.0 + - - +
157B TYR* 3.9 29.1 + - - +
86C ARG* 4.0 17.0 - - - +
90C GLU* 5.9 1.8 - - - -
93C ARG* 6.2 0.2 - - - -
69J ARG* 3.5 37.8 + - - +
70J GLU* 2.6 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 3.8 43.9 + - + +
111B ILE 3.2 13.2 + - - +
112B LEU 3.7 7.6 - - - +
113B VAL 3.3 0.2 - - - -
114B ARG* 1.3 72.5 - - - +
116B LEU* 1.3 68.1 + - + +
118B ASP* 3.0 41.4 + - - +
119B ILE* 3.1 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.0 2.5 - - + -
76B VAL* 5.8 0.2 - - + -
88B LEU* 3.5 45.1 - - + +
89B ILE* 5.5 0.4 - - - -
91B THR* 4.0 11.9 - - - +
92B ALA* 3.7 25.1 - - + -
112B LEU* 3.3 11.9 + - + +
113B VAL 3.8 4.0 - - - +
115B ARG* 1.3 78.1 - - + +
117B SER* 1.3 63.0 + - - +
119B ILE* 3.1 19.0 + - + +
120B LYS* 3.2 18.9 + - + +
136B PHE* 4.2 13.9 - - + -
138B TYR* 3.4 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL 3.0 19.1 + - - -
114B ARG 3.7 3.4 - - - -
116B LEU* 1.3 75.6 - - - +
118B ASP* 1.3 56.9 + - - +
120B LYS* 3.2 7.2 + - - +
121B GLN* 2.8 27.0 + - - +
138B TYR* 4.9 0.4 + - - -
151B SER* 3.6 11.8 - - - -
155B GLY* 3.4 22.8 - - - -
157B TYR* 3.5 27.3 - - - +
86C ARG* 3.3 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.0 33.4 + - - +
115B ARG* 3.0 27.7 + - - +
117B SER* 1.3 72.8 - - - +
119B ILE* 1.3 65.4 + - - +
121B GLN* 3.5 6.7 + - - +
122B GLY* 3.0 19.8 + - - -
86C ARG* 2.9 30.1 + - - +
87C ILE* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.0 20.0 - - + -
91B THR* 3.5 29.6 - - + +
115B ARG* 3.1 46.2 + - + +
116B LEU* 3.1 17.7 + - + +
118B ASP* 1.3 76.2 - - - +
120B LYS* 1.3 62.7 + - - +
122B GLY* 3.3 9.6 + - - -
123B TYR* 3.3 31.2 + - + -
132B PHE* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.8 32.1 - - + -
116B LEU* 3.2 17.8 + - + +
117B SER* 3.4 14.4 - - - +
119B ILE* 1.3 74.5 - - - +
121B GLN* 1.3 67.2 + - - +
122B GLY 3.2 0.9 + - - -
123B TYR* 3.2 14.2 + - - +
124B THR* 3.5 10.6 + - - -
131B PRO* 5.6 0.9 - - - +
132B PHE* 4.5 17.9 - - + +
134B VAL* 3.8 18.1 + - - -
136B PHE* 3.4 16.0 - - - -
138B TYR* 5.2 0.4 - - - +
151B SER* 2.7 43.9 + - - +
152B ASN 3.7 11.0 - - - +
153B PRO* 4.1 14.5 - - + +
155B GLY* 3.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.8 19.8 + - - +
118B ASP* 3.6 10.1 + - - +
120B LYS* 1.3 72.5 - - - +
122B GLY* 1.3 65.9 + - - +
124B THR* 2.8 24.9 + - + -
125B GLN* 3.1 30.7 + - - +
126B HIS* 5.5 1.8 + - - -
154B SER 3.7 14.1 - - - +
155B GLY* 3.9 1.0 - - - -
83C ALA* 3.5 36.6 - - + +
84C ASP* 3.1 19.2 - - - +
86C ARG* 4.4 2.0 - - - +
87C ILE* 3.5 28.6 - - + +
130C ARG* 4.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP 3.0 14.2 + - - -
119B ILE* 3.7 6.1 - - - -
120B LYS 3.1 1.0 - - - -
121B GLN* 1.3 84.4 - - - +
123B TYR* 1.3 57.0 + - - +
124B THR 3.0 0.2 - - - -
125B GLN* 2.9 17.7 + - - -
126B HIS* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 3.7 20.0 + - - -
13B THR* 4.3 9.7 + - - -
119B ILE* 3.3 23.1 - - + -
120B LYS 3.2 8.8 + - - +
122B GLY* 1.3 76.2 - - - +
124B THR* 1.3 58.2 + - - +
125B GLN 3.3 0.4 + - - -
126B HIS 4.1 12.3 - - - +
129B LEU* 3.8 48.8 + - + +
130B ARG 3.5 17.3 - - - +
131B PRO* 4.2 21.4 - - + +
132B PHE* 3.5 31.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 3.7 14.3 - - - +
21B LEU* 3.7 17.8 - - + +
24B VAL* 3.5 22.4 - - - +
120B LYS 3.5 2.2 + - - -
121B GLN* 2.8 18.6 - - - +
123B TYR* 1.3 78.3 - - - +
125B GLN* 1.3 55.4 + - - +
131B PRO* 5.2 3.4 - - - +
153B PRO 3.7 14.9 + - - -
154B SER 3.8 10.4 + - - +
81C LEU* 5.5 0.2 - - + -
83C ALA* 6.2 0.2 - - + -
84C ASP* 4.4 3.4 - - - +
130C ARG* 2.8 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 4.7 5.4 - - - -
121B GLN* 3.1 33.1 + - - +
122B GLY 2.9 5.8 + - - +
124B THR* 1.3 80.3 - - - +
126B HIS* 1.3 67.5 + - + +
84C ASP* 4.6 0.2 - - - -
87C ILE* 4.9 3.8 - - - +
123C TYR* 3.4 25.7 + - + -
128C GLY 3.8 0.2 - - - +
129C VAL* 3.2 5.7 - - - +
130C ARG* 3.1 61.1 + - + +
131C PRO 3.7 5.9 - - - +
132C PHE* 3.6 32.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 4.8 2.2 - - - -
121B GLN* 5.5 1.6 + - - -
122B GLY* 3.0 33.2 + - - +
123B TYR* 4.1 13.2 + - - +
124B THR 4.0 0.4 - - - -
125B GLN* 1.3 92.9 + - + +
127B GLY* 1.3 60.8 + - - +
128B GLY 3.5 5.0 + - - -
129B LEU* 4.8 1.9 + - - +
123C TYR* 4.8 13.7 + + - -
128C GLY 3.2 13.2 - - - +
129C VAL* 3.6 18.6 - - + -
----------------------------------------------------------
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