Contacts of the helix formed by residues 108 - 120 (chain B) in PDB entry 1ADI
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 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 1.3 77.2 - - - +
109B TYR* 1.3 57.2 + - - +
111B VAL* 3.3 8.7 + - - +
112B ALA* 2.8 28.6 + - - +
181B VAL* 3.8 19.8 - - + +
185B LYS* 2.8 35.4 + - - -
186B VAL* 3.9 13.2 - - + +
189B ASP* 4.5 0.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
107B LEU* 3.8 27.3 - - + +
108B ASP* 1.3 72.6 - - - +
110B HIS* 1.3 83.6 + + - +
112B ALA* 3.6 1.3 - - - -
113B LEU* 2.7 40.3 + - + +
139B ASP* 4.0 1.9 + - - -
145B GLY* 6.1 0.2 - - - -
146B LEU* 3.7 26.0 - - - +
161B LEU* 4.3 3.6 - - + -
164B VAL* 3.8 13.7 - - + +
165B MET* 3.8 36.3 - - + -
168B HIS* 2.9 50.0 - + + -
169B ASN* 5.5 0.9 - - - +
172B LEU* 4.6 1.6 - - + -
181B VAL* 3.8 26.4 - - + +
186B VAL* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU 3.1 22.4 + - - -
106B ILE* 3.6 5.5 - - + -
107B LEU* 3.0 28.4 + - + +
109B TYR* 1.3 99.3 - + - +
111B VAL* 1.3 65.2 + - - +
113B LEU* 3.4 1.9 + - + +
114B ASP 3.3 10.6 + - - -
132B GLY* 3.6 16.6 - - - +
135B PRO* 3.2 53.2 + - + +
136B ALA* 3.8 9.5 - - - +
139B ASP* 2.8 29.8 + - + -
145B GLY* 6.3 1.3 - - - -
146B LEU* 6.3 0.9 - - + -
168B HIS* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 5.5 2.2 - - - +
75B SER* 5.6 1.8 - - - +
106B ILE* 4.3 12.1 - - + -
107B LEU 3.4 4.9 + - - +
108B ASP* 3.3 10.9 + - - +
110B HIS* 1.3 77.7 - - - +
112B ALA* 1.3 60.9 + - - +
113B LEU 3.2 0.2 + - - -
114B ASP* 3.3 2.8 + - - +
115B ASN* 2.9 39.5 + - - +
131B ARG* 3.1 41.0 - - + +
132B GLY* 4.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP 2.8 19.0 + - - +
109B TYR 3.6 4.5 - - - +
111B VAL* 1.3 78.6 - - - +
113B LEU* 1.3 56.9 + - - +
115B ASN* 3.6 9.5 - - - +
116B ALA* 3.6 14.7 + - - +
172B LEU* 3.8 17.0 - - + +
179B GLU 5.6 1.1 - - - +
181B VAL* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR 2.7 31.2 + - - +
110B HIS* 3.5 5.6 - - - +
111B VAL 3.2 0.2 - - - -
112B ALA* 1.3 75.2 - - - +
114B ASP* 1.3 66.7 + - - +
116B ALA* 3.6 4.3 + - - +
117B ARG* 3.1 43.5 + - - +
135B PRO* 3.7 24.7 - - + -
138B GLU* 5.7 0.9 - - - +
168B HIS* 3.8 42.2 - - + +
171B GLN* 4.8 11.0 - - + +
172B LEU* 3.9 30.5 - - + -
176B TYR* 5.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B HIS 3.3 2.7 + - - +
111B VAL 3.3 7.3 + - - +
113B LEU* 1.3 74.4 - - - +
115B ASN* 1.3 72.1 + - - +
116B ALA 2.9 1.4 + - - -
117B ARG* 2.9 27.7 + - - +
118B GLU* 3.0 15.5 + - - +
128B THR* 4.6 9.4 + - - -
131B ARG* 3.7 12.4 - - - -
132B GLY* 2.7 33.7 + - - +
133B ILE* 4.2 1.2 + - - +
134B GLY 4.6 1.4 + - - -
135B PRO* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 2.9 26.4 + - - +
112B ALA* 3.6 11.9 - - - +
114B ASP* 1.3 77.1 - - - +
116B ALA* 1.3 57.9 + - - +
118B GLU* 2.9 29.9 + - - +
119B LYS* 3.3 15.7 + - - +
131B ARG* 4.1 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 3.6 9.3 + - - +
113B LEU 3.6 8.0 + - - +
114B ASP 2.9 1.8 + - - -
115B ASN* 1.3 75.1 - - - +
117B ARG* 1.3 56.5 + - - +
118B GLU 2.9 5.6 - - - -
119B LYS* 3.1 25.1 + - - +
120B ALA* 2.9 31.5 + - - +
172B LEU* 4.9 3.1 - - + -
176B TYR* 3.7 34.7 - - + -
178B ALA* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.7 4.1 + - - +
144A ARG* 3.6 21.2 - - - +
167A TYR* 4.2 8.9 + - - -
113B LEU* 3.1 34.8 + - - +
114B ASP* 2.9 22.4 + - - +
116B ALA* 1.3 72.9 - - - +
118B GLU* 1.3 55.2 + - - +
120B ALA 4.1 1.3 - - - -
121B ARG* 3.3 42.1 + - - +
125B ALA* 5.8 0.2 - - - -
135B PRO* 4.1 16.8 - - - +
138B GLU* 2.6 42.0 + - - -
171B GLN* 5.4 2.0 - - - +
176B TYR* 3.8 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.0 13.5 - - + +
115B ASN* 2.9 23.6 - - - +
117B ARG* 1.3 77.6 - - + +
119B LYS* 1.3 56.7 + - - +
120B ALA 3.1 1.3 - - - -
121B ARG* 2.9 3.2 + - - +
122B GLY* 2.7 35.0 + - - -
125B ALA* 4.3 20.3 - - + +
126B ILE 5.9 0.4 - - - +
127B GLY* 6.2 0.7 - - - +
128B THR* 2.9 34.9 - - + +
131B ARG* 3.0 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.3 11.2 + - - +
116B ALA* 3.1 24.9 + - - +
118B GLU* 1.3 78.7 + - - +
120B ALA* 1.3 60.8 + - - +
121B ARG 3.4 0.9 + - - -
122B GLY* 4.0 6.9 + - - +
176B TYR 5.5 4.9 + - - +
177B LYS 5.5 0.2 + - - -
178B ALA* 3.7 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 2.9 15.8 + - - +
117B ARG* 4.5 0.7 - - - -
118B GLU 3.1 0.4 - - - -
119B LYS* 1.3 78.4 - - - +
121B ARG* 1.3 83.5 + - - +
176B TYR* 4.7 11.4 - - + -
----------------------------------------------------------
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