Contacts of the helix formed by residues 127 - 143 (chain B) in PDB entry 1DIZ
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 SER 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 1.3 80.3 - - - +
128B VAL* 1.3 66.1 + - - +
129B ALA* 3.7 9.0 + - - +
130B MET* 2.9 18.7 + - - +
131B ALA* 2.9 21.1 + - - +
7C A 3.4 33.3 + - - -
8C NRI 3.4 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 4.1 16.4 - - + +
22B ARG* 3.7 50.0 - - + +
126B VAL 4.0 0.2 + - - -
127B SER* 1.3 72.9 - - - +
129B ALA* 1.3 61.5 + - - +
131B ALA* 3.4 7.2 + - + +
132B ALA* 3.0 23.4 + - - +
8C NRI 3.5 17.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
21B ALA 5.3 3.1 - - - -
127B SER* 3.1 8.1 + - - +
128B VAL* 1.3 79.2 - - - +
130B MET* 1.3 62.1 - - - +
132B ALA* 3.4 8.2 + - - +
133B LYS* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.4 31.0 - - + -
127B SER* 2.9 17.8 + - - +
129B ALA* 1.3 76.4 - - - +
131B ALA* 1.3 65.7 + - - +
133B LYS* 3.1 10.6 + - + +
134B LEU* 2.9 54.4 + - + +
137B ARG* 5.3 5.2 - - - -
173B GLY 5.8 0.7 - - - +
20D C 3.9 28.0 - - - +
21D A 3.9 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG 5.6 0.4 - - - +
122B LEU* 3.3 27.4 - - + +
123B GLY* 4.0 12.8 - - - +
126B VAL* 3.6 6.7 - - + +
127B SER 2.9 14.9 + - - +
128B VAL* 3.7 9.2 - - + +
130B MET* 1.3 77.1 - - - +
132B ALA* 1.3 58.0 + - - +
134B LEU* 3.7 4.1 - - - +
135B THR* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 4.3 15.3 - - - +
22B ARG* 4.5 10.1 - - - +
23B ALA 4.4 16.6 - - - +
24B VAL* 5.2 2.0 - - - -
128B VAL 3.0 17.5 + - - +
129B ALA* 3.5 8.3 - - - +
130B MET 3.1 0.2 - - - -
131B ALA* 1.3 75.5 - - - +
133B LYS* 1.3 64.4 + - - +
135B THR* 3.5 4.8 + - - -
136B ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.2 10.0 + - - +
130B MET* 3.1 19.3 + - + +
132B ALA* 1.3 77.5 - - - +
134B LEU* 1.3 66.7 + - + +
136B ALA* 3.1 8.0 + - - +
137B ARG* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.0 44.4 - - + +
126B VAL* 4.9 9.0 - - + -
130B MET* 2.9 54.4 + - + +
131B ALA* 3.7 6.3 - - - +
133B LYS* 1.3 77.3 - - - +
135B THR* 1.3 58.4 + - - +
137B ARG* 3.2 16.2 + - - +
138B VAL* 2.9 31.4 + - - +
172B LEU* 5.2 5.3 - - + +
173B GLY 4.6 15.9 - - - +
174B MET* 4.2 21.3 - - + +
175B PRO* 6.0 0.9 - - + -
178B ARG* 5.8 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.4 26.9 - - + -
118B VAL* 5.2 0.2 - - + -
119B ARG* 4.4 17.7 + - + +
122B LEU* 3.1 27.6 - - + +
131B ALA* 3.0 18.6 + - - +
132B ALA* 3.9 5.2 - - - -
134B LEU* 1.3 75.9 - - - +
136B ALA* 1.3 57.5 + - - +
138B VAL* 3.3 4.2 + - + +
139B ALA* 2.8 28.1 + - - +
155B PHE* 3.7 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.7 18.8 - - + +
25B SER* 4.3 21.8 - - - +
132B ALA 3.1 13.3 + - - +
133B LYS* 3.1 11.6 + - - +
135B THR* 1.3 77.1 - - - +
137B ARG* 1.3 54.8 + - + +
139B ALA* 2.9 3.2 + - - +
140B GLN* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B MET* 5.3 5.1 - - - -
133B LYS* 2.9 28.7 + - - +
134B LEU* 3.5 19.9 - - - +
136B ALA* 1.3 75.7 - - + +
138B VAL* 1.3 65.3 + - - +
140B GLN* 3.2 7.1 + - - +
141B LEU* 3.1 25.5 + - - +
172B LEU* 2.6 58.4 + - + +
173B GLY* 4.3 5.3 - - - -
20D C 5.3 8.7 + - - -
21D A 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.1 10.3 - - + -
122B LEU* 4.1 10.8 - - + -
134B LEU 2.9 16.5 + - - +
135B THR* 3.5 10.1 - - + +
137B ARG* 1.3 76.4 - - - +
139B ALA* 1.3 58.7 + - - +
141B LEU 3.3 0.2 + - - -
142B TYR* 2.9 42.0 + - + +
155B PHE* 5.7 1.6 - - + -
156B PRO* 4.0 15.5 - - + -
161B LEU* 4.4 16.2 - - + -
169B LEU* 4.1 5.6 - - + -
172B LEU* 3.9 13.5 - - + -
174B MET* 3.8 28.7 - - + -
182B LEU* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 4.0 18.6 - - + -
25B SER 5.1 0.2 - - - +
27B VAL* 4.2 13.0 - - + -
135B THR 2.8 18.7 + - - +
136B ALA* 2.9 4.9 + - - +
138B VAL* 1.3 77.4 - - - +
140B GLN* 1.3 59.5 + - - +
143B GLY* 2.9 24.1 + - - -
153B ILE* 3.0 15.4 - - + +
155B PHE* 5.1 2.5 - - + -
156B PRO* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.9 25.6 + - - -
26B SER* 4.7 10.9 + - - -
136B ALA* 2.7 31.9 + - - +
137B ARG* 3.2 8.0 + - - +
139B ALA* 1.3 75.1 - - - +
141B LEU* 1.3 58.3 - - + +
143B GLY 4.7 3.3 - - - +
145B ARG* 5.7 7.3 + - - +
153B ILE* 4.0 13.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
137B ARG 3.1 15.8 + - - +
138B VAL 3.8 2.7 - - - +
140B GLN* 1.3 80.4 - - + +
142B TYR* 1.3 97.4 + - + +
143B GLY 3.8 0.9 - - - -
160B ARG* 4.2 9.9 + - - -
168B ALA* 4.4 10.3 - - + +
172B LEU* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 2.9 19.9 + - + +
141B LEU* 1.3 104.2 - - + +
143B GLY* 1.3 61.0 + - - +
144B GLU* 5.2 0.7 - - - +
156B PRO* 3.9 22.2 - - + +
157B THR 4.7 0.3 + - - -
160B ARG* 3.2 54.0 + - + +
161B LEU* 4.0 11.4 - - + -
164B ALA* 3.5 33.5 - - + +
165B ASP 4.1 1.4 + - - -
168B ALA* 3.3 28.9 - - - +
169B LEU* 3.3 30.6 - - + +
172B LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ALA 2.9 13.8 + - - -
140B GLN 4.9 3.3 - - - +
141B LEU 5.2 0.3 - - - -
142B TYR* 1.3 82.1 + - - +
144B GLU* 1.3 63.6 + - - -
145B ARG* 4.1 2.1 + - - +
153B ILE* 3.8 10.4 - - - +
154B CYS 3.3 19.3 - - - -
156B PRO* 3.8 10.8 - - - +
160B ARG* 4.6 4.9 + - - -
----------------------------------------------------------
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