Contacts of the helix formed by residues 135 - 151 (chain B) in PDB entry 4UN0
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 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE 3.7 2.7 - - - -
134B ASP* 1.3 81.5 - - - +
136B PRO* 1.3 67.2 - - - +
137B LYS* 3.3 10.0 + - - +
138B GLU* 3.2 25.2 + - + +
139B GLU* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.7 26.9 - - + -
129B PHE* 3.9 20.2 - - + -
132B PHE* 3.5 40.8 - - + +
133B GLY 5.1 1.1 - - - +
134B ASP 3.7 6.7 - - - +
135B ASP* 1.3 89.8 - - - +
137B LYS* 1.3 63.1 + - - +
139B GLU* 3.2 2.9 + - + +
140B VAL* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B CYS* 3.8 24.1 - - + +
114B LYS* 4.9 15.3 - - + +
117B ILE* 3.4 15.9 - - + +
135B ASP* 3.3 8.3 + - - +
136B PRO* 1.3 79.1 - - - +
138B GLU* 1.3 58.8 + - - +
140B VAL* 3.1 4.0 + - - +
141B MET* 2.9 59.2 + - + +
764D LYS* 5.5 4.9 - - - +
765D GLU* 4.8 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP* 3.2 28.8 + - + +
137B LYS* 1.3 79.7 - - - +
139B GLU* 1.3 60.9 + - - +
141B MET* 4.3 7.0 - - - -
142B VAL* 3.1 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.2 17.3 - - + +
131B GLN 5.6 0.7 - - - +
132B PHE* 4.0 18.2 - - - +
135B ASP 3.2 12.9 + - - +
136B PRO* 3.2 10.0 + - + +
137B LYS 3.2 0.2 - - - -
138B GLU* 1.3 77.1 - - - +
140B VAL* 1.3 60.0 + - - +
142B VAL* 4.4 3.6 - - - +
143B LEU* 3.7 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.3 13.2 - - + +
97B ALA* 4.6 7.6 - - + +
98B CYS* 3.7 31.7 - - - +
101B PHE* 5.0 10.1 - - + -
113B CYS* 4.5 16.6 - - - -
117B ILE* 5.2 6.3 - - + -
132B PHE* 4.2 24.7 - - + -
136B PRO 3.0 15.1 + - - +
137B LYS* 3.6 6.5 - - - +
139B GLU* 1.3 78.7 - - - +
141B MET* 1.3 65.9 + - - +
143B LEU* 3.2 14.7 + - - +
144B GLU* 3.2 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 4.3 11.4 - - + -
113B CYS* 3.6 33.0 - - + -
137B LYS* 2.9 40.4 + - + +
138B GLU* 3.6 6.9 + - - +
140B VAL* 1.3 78.5 - - - +
142B VAL* 1.3 63.9 + - + +
144B GLU* 3.3 23.0 + - - +
145B ARG* 4.0 2.6 + - - +
760D LEU* 5.9 2.3 - - - +
764D LYS* 5.4 0.4 - - - -
765D GLU* 3.6 34.1 - - - +
766D GLY* 3.9 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.1 21.1 + - + +
139B GLU* 4.4 4.3 - - - +
141B MET* 1.3 77.5 - - + +
143B LEU* 1.3 63.7 + - - +
144B GLU 3.2 1.0 + - - -
145B ARG* 3.3 20.4 + - - +
146B ILE* 3.9 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.1 21.1 - - + -
90B PHE* 5.0 12.1 - - + -
94B VAL* 4.1 17.0 - - + +
95B THR* 3.7 41.7 - - + +
98B CYS* 3.9 9.9 - - + -
139B GLU 3.7 10.8 + - - +
140B VAL 3.2 10.8 + - - +
142B VAL* 1.3 77.0 - - - +
144B GLU* 1.3 60.2 + - - +
146B ILE* 3.0 29.2 + - + -
147B LEU* 2.8 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B CYS* 3.6 16.1 - - - -
101B PHE* 3.7 15.1 - - + -
102B LEU* 4.1 15.3 - - + +
105B LYS* 2.5 34.3 + - - -
140B VAL 3.2 11.0 + - - +
141B MET* 3.4 16.1 - - - +
142B VAL 3.1 0.4 - - - -
143B LEU* 1.3 77.0 - - - +
145B ARG* 1.3 61.6 + - - +
147B LEU* 3.7 2.3 - - - +
148B LEU* 3.1 35.4 + - + +
760D LEU* 6.0 1.2 - - - +
765D GLU 3.9 1.0 - - - +
766D GLY* 3.8 8.7 - - - -
767D PHE* 3.3 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B MET 4.0 2.3 + - - +
142B VAL* 3.3 12.2 + - - +
143B LEU 3.2 0.4 - - - -
144B GLU* 1.3 77.5 - - - +
146B ILE* 1.3 64.4 + - + +
148B LEU* 3.9 1.7 + - - -
149B GLN* 3.4 30.6 + - - +
760D LEU* 4.6 14.1 - - + +
809D PHE* 3.8 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.3 8.7 - - + -
85B HIS* 4.0 18.4 - - + +
90B PHE* 4.9 15.5 - - + -
142B VAL* 4.1 15.3 - - + +
143B LEU* 3.0 30.4 + - + +
145B ARG* 1.3 77.3 - - + +
147B LEU* 1.3 59.3 + - - +
149B GLN* 3.3 15.4 + - - +
150B THR* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.3 5.8 - - + +
81B PHE* 3.7 33.4 - - + -
95B THR* 5.5 1.3 - - + -
98B CYS* 3.9 17.5 - - + +
99B CYS* 3.9 41.7 - - - -
102B LEU* 3.7 26.9 - - + -
143B LEU* 2.8 17.0 + - + +
144B GLU* 3.3 6.9 + - - +
146B ILE* 1.3 78.5 - - - +
148B LEU* 1.3 61.6 + - - +
150B THR* 3.3 1.0 + - - -
151B ILE* 3.0 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.7 34.1 - - + -
144B GLU* 3.1 27.2 + - + +
145B ARG* 4.1 3.8 - - - +
146B ILE 3.3 0.2 - - - -
147B LEU* 1.3 77.5 - - - +
149B GLN* 1.3 61.6 + - - +
151B ILE* 3.4 4.4 - - + +
152B LYS* 3.1 2.9 + - - -
153B PHE* 3.1 57.3 + - + -
155B LEU* 4.0 19.3 - - + -
767D PHE* 4.0 40.6 - - + -
772D ILE* 6.1 0.9 - - + -
809D PHE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 3.4 20.0 + - - +
146B ILE* 3.3 18.1 + - + +
148B LEU* 1.3 74.4 - - - +
150B THR* 1.3 66.5 - - - +
152B LYS* 3.1 18.4 + - - +
153B PHE* 4.9 6.3 - - + -
723D CYS 5.4 1.7 + - - -
794D THR* 3.4 30.1 - - - +
809D PHE* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 5.6 0.4 - - - +
24B TRP* 3.7 11.1 - - - -
80B ARG 4.4 0.9 - - - +
81B PHE* 4.1 20.7 - - - +
84B PHE* 3.6 45.1 - - + -
85B HIS* 2.9 28.8 + - + +
146B ILE* 2.8 23.1 + - - +
147B LEU 3.3 4.9 + - - -
149B GLN* 1.3 79.7 - - - +
151B ILE* 1.3 58.3 + - + +
152B LYS* 3.3 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.1 25.0 - - + -
77B TYR* 4.3 33.7 - - + +
80B ARG* 4.9 14.1 - - + +
81B PHE 5.4 0.4 - - - +
102B LEU* 3.9 19.5 - - + -
147B LEU* 3.0 34.5 + - + +
148B LEU* 3.4 12.1 - - - +
150B THR* 1.3 77.7 - - + +
152B LYS* 1.3 66.1 + - - +
153B PHE* 3.8 4.5 - - - +
154B ASP* 3.0 16.9 + - - +
155B LEU* 3.8 26.9 - - + -
----------------------------------------------------------
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