Contacts of the helix formed by residues 123 - 142 (chain B) in PDB entry 1DKE
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 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.7 3.4 - - - +
120B LYS* 3.6 17.0 + - + +
121B GLU* 3.1 9.5 + - - +
122B PHE* 1.3 78.0 - - - +
124B PRO* 1.3 70.1 - - + +
125B PRO* 3.3 11.3 - - - +
126B VAL* 3.0 28.7 + - + +
127B GLN* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.8 7.6 - - + +
30A GLU* 4.1 23.6 - - + +
31A ARG* 3.7 43.9 - - + +
34A LEU* 3.8 21.3 - - + +
35A SER* 5.0 0.9 + - - -
50A HIS* 6.2 0.7 - - + -
123B THR* 1.3 85.1 - - + +
125B PRO* 1.3 74.6 - - + +
127B GLN* 3.2 4.0 + - + +
128B ALA* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 5.7 1.1 - - - +
34A LEU* 4.1 14.1 - - + -
7B GLU* 4.9 5.5 - - - +
123B THR* 3.3 12.6 - - - +
124B PRO* 1.3 104.2 - - + +
126B VAL* 1.4 60.4 + - + +
128B ALA* 3.6 5.6 + - + +
129B ALA* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 4.3 26.9 - - + +
11B VAL* 6.1 0.2 - - + -
14B LEU* 4.3 8.7 - - + -
121B GLU 4.2 11.0 - - - +
122B PHE* 3.9 21.1 - - + -
123B THR* 3.0 27.5 + - + +
125B PRO* 1.4 74.5 - - + +
127B GLN* 1.3 67.4 + - - +
129B ALA* 3.3 8.0 + - + +
130B TYR* 2.9 38.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 2.8 50.0 + - - +
35A SER* 3.7 15.1 + - - +
103A HIS* 4.1 1.4 + - - -
104A CYS* 3.9 19.8 - - - -
107A VAL* 3.5 19.4 - - - +
111B VAL* 4.4 1.1 - - + -
122B PHE* 3.9 23.7 - - + -
123B THR 2.9 12.4 + - - +
124B PRO 3.4 8.3 - - - +
126B VAL* 1.3 77.7 - - - +
128B ALA* 1.4 57.8 + - - +
130B TYR* 3.0 2.6 + - - +
131B GLN* 2.7 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.8 13.7 - - + +
35A SER* 3.7 33.1 - - - +
7B GLU* 4.4 9.2 - - - +
124B PRO 2.9 15.8 + - - +
125B PRO* 3.6 6.0 + - + +
126B VAL 3.3 0.4 - - - -
127B GLN* 1.4 79.1 - - - +
129B ALA* 1.3 59.2 + - - +
131B GLN* 3.4 5.3 + - - +
132B LYS* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.6 8.4 - - + +
7B GLU* 3.6 41.7 + - + +
10B ALA* 5.4 2.0 - - + -
11B VAL* 3.8 18.6 - - + -
125B PRO 3.5 8.4 + - - +
126B VAL* 3.3 10.4 + - + +
128B ALA* 1.3 74.9 - - - +
130B TYR* 1.4 58.2 + - - +
132B LYS* 2.9 20.4 + - - +
133B VAL* 3.0 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 2.6 53.0 + - + +
14B LEU* 3.6 25.1 - - + +
15B TRP* 3.5 34.0 + + - +
71B PHE* 5.7 3.4 - + - -
75B LEU* 4.3 6.5 - - + -
110B LEU* 5.9 0.4 - - + -
111B VAL* 4.2 9.9 - - + -
114B LEU* 4.0 17.7 - - + -
122B PHE* 3.9 25.1 - + + -
126B VAL* 2.9 28.3 + - + +
127B GLN 3.7 5.2 - - - +
129B ALA* 1.4 67.4 - - - +
131B GLN* 1.4 67.6 + - - +
133B VAL* 3.0 14.4 + - + +
134B VAL* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.6 24.5 - - - +
36A PHE* 4.1 20.8 - - + -
103A HIS* 2.8 24.4 + - - -
108B ASN* 3.3 23.0 + - - +
111B VAL* 3.2 21.7 - - - +
127B GLN* 2.7 43.1 + - + +
128B ALA* 3.7 5.8 - - - +
130B TYR* 1.4 72.2 - - - +
132B LYS* 1.3 62.4 + - + +
134B VAL* 3.5 2.8 + - - +
135B ALA* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B VAL* 3.2 15.4 - - + +
2B HIS 3.0 30.9 + - - +
3B LEU* 3.4 17.5 - - + -
4B THR* 4.5 4.6 + - - +
7B GLU* 2.7 36.7 + - - +
128B ALA* 3.1 16.4 + - - +
129B ALA 2.9 6.0 + - - +
131B GLN* 1.3 72.6 - - + +
133B VAL* 1.3 64.7 + - - +
135B ALA* 4.0 3.8 - - - +
136B GLY 3.1 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B VAL* 4.5 6.1 - - - +
3B LEU* 4.1 9.2 - - + -
11B VAL* 4.0 29.2 - - + -
71B PHE* 4.4 7.2 - - + -
75B LEU* 3.6 33.0 - - + -
78B LEU* 4.4 14.6 - - + -
81B LEU* 4.8 0.7 - - - +
129B ALA 3.0 14.5 + - - +
130B TYR* 3.3 15.9 - - + +
132B LYS* 1.3 78.2 - - - +
134B VAL* 1.3 58.4 - - + +
136B GLY* 3.2 2.4 + - - -
137B VAL* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.3 15.3 - - + -
103B PHE 4.6 4.3 - - - +
104B ARG* 4.9 4.0 - - + +
107B GLY* 2.9 50.5 - - - +
108B ASN* 5.1 4.3 - - - +
110B LEU* 4.3 19.3 - - + -
111B VAL* 4.2 12.1 - - + -
130B TYR* 2.8 27.2 + - + +
131B GLN* 4.1 2.0 - - - +
133B VAL* 1.3 73.5 - - + +
135B ALA* 1.3 62.9 + - - +
137B VAL* 3.5 2.8 + - + +
138B ALA* 3.1 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 6.3 2.7 - - - -
131B GLN 3.2 17.0 + - - +
132B LYS* 4.0 4.5 - - - +
134B VAL* 1.3 76.8 - - - +
136B GLY* 1.3 56.0 + - - +
138B ALA* 3.3 6.2 + - - +
139B ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B VAL* 3.3 26.9 - - - +
81B LEU* 3.7 9.3 - - - +
132B LYS 3.1 11.5 + - - -
135B ALA* 1.3 70.9 - - - +
137B VAL* 1.3 60.2 + - - +
139B ASN* 3.3 9.2 + - - +
140B ALA* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.8 39.7 - - + -
75B LEU* 4.6 6.1 - - + -
81B LEU* 3.9 10.9 - - + +
85B PHE* 4.0 29.5 - - + -
133B VAL* 2.9 29.7 + - + +
134B VAL 3.8 4.9 - - - +
136B GLY* 1.3 75.9 - - - +
138B ALA* 1.3 58.0 + - - +
140B ALA* 3.2 6.7 + - - +
141B LEU* 2.9 41.6 + - + +
147B HEM 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 5.3 1.1 - - - +
103B PHE* 3.9 39.3 - - + +
104B ARG* 4.1 12.1 - - + +
134B VAL* 3.1 19.6 + - + +
135B ALA* 3.8 4.7 - - - +
137B VAL* 1.3 74.8 - - - +
139B ASN* 1.3 60.5 + - - +
141B LEU* 3.3 3.8 + - - +
142B ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 2.8 39.3 + - - +
135B ALA 2.9 20.7 + - - +
136B GLY* 3.7 9.4 - - - +
138B ALA* 1.3 72.5 - - - +
140B ALA* 1.4 63.6 + - - +
142B ALA* 3.3 6.5 + - - +
143B HIS* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.6 39.5 - - + +
82B LYS* 3.8 17.6 - - + +
85B PHE* 4.1 13.3 - - + +
86B ALA* 5.5 0.2 - - - -
89B SER* 3.9 8.1 + - - -
136B GLY 2.8 18.8 + - - +
137B VAL 3.6 4.0 - - - +
139B ASN* 1.4 77.6 + - - +
141B LEU* 1.4 60.9 + - - +
143B HIS* 3.3 16.5 + - - +
144B LYS* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.0 19.5 - - + -
88B LEU* 3.8 37.2 - - + +
89B SER* 2.8 23.5 + - - -
92B HIS* 4.7 5.6 - - + +
103B PHE* 3.8 31.5 - - + -
137B VAL* 2.9 26.9 + - + +
138B ALA 4.0 1.1 - - - +
140B ALA* 1.4 74.9 - - - +
142B ALA* 1.3 59.0 + - - +
145B TYR* 3.5 11.4 - - - -
147B HEM 3.3 47.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 3.7 26.9 - - + -
138B ALA 2.9 17.7 + - - +
139B ASN* 3.3 7.2 + - - +
140B ALA 3.2 0.4 - - - -
141B LEU* 1.3 80.4 - - - +
143B HIS* 1.3 61.3 + - - +
144B LYS 3.4 1.8 - - - -
145B TYR* 3.2 28.0 + - - +
38C THR* 5.8 1.5 - - + +
----------------------------------------------------------
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