Contacts of the helix formed by residues 137 - 152 (chain B) in PDB entry 4MSP
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 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASN* 6.3 0.4 - - - -
135B LYS 4.1 0.4 + - - -
136B LEU* 1.3 75.3 - - - +
138B LYS* 1.3 65.1 + - - +
139B ASP* 3.5 8.5 + - - +
140B GLU* 3.0 38.6 + - - +
141B VAL* 3.0 22.0 + - - +
169B PHE* 3.5 2.9 - - - -
178B GLY 4.6 0.4 - - - -
179B PHE* 3.7 28.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 1.3 72.9 - - - +
139B ASP* 1.3 60.6 + - - +
141B VAL* 3.2 2.6 + - - +
142B LYS* 2.9 30.2 + - - +
165B VAL* 3.9 13.4 - - + +
166B GLU* 2.9 43.2 + - - +
169B PHE* 3.5 47.6 - - + -
170B ASP* 5.9 0.2 + - - -
178B GLY* 4.4 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 3.2 8.9 + - - +
138B LYS* 1.3 78.2 - - - +
140B GLU* 1.3 61.2 + - + +
142B LYS* 3.8 13.4 + - - +
143B ALA* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.6 19.0 - - - +
129B ASP* 3.7 2.4 - - - +
130B LEU* 3.2 24.6 + - + +
131B ASN* 2.9 31.3 + - - +
135B LYS 3.1 4.0 - - - +
136B LEU* 3.3 6.3 - - + -
137B SER* 3.0 38.2 + - - +
139B ASP* 1.3 77.4 - - + +
141B VAL* 1.3 63.3 + - - +
143B ALA* 3.4 6.3 + - - +
144B TYR* 3.1 23.0 + - - +
201B CA 2.4 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A 1PE 4.5 9.0 - - - +
206A PGO 3.8 28.7 - - + -
128B MET* 5.1 4.7 - - + -
136B LEU* 4.1 15.5 - - + -
137B SER 3.0 19.6 + - - +
138B LYS 3.8 3.1 - - - +
140B GLU* 1.3 77.5 - - - +
142B LYS* 1.3 62.7 + - - +
144B TYR* 3.3 6.8 + - - +
145B LEU* 3.0 39.1 + - + +
165B VAL* 4.2 7.6 - - + -
168B ILE* 4.6 8.1 - - + -
169B PHE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS 2.9 17.7 + - - +
139B ASP* 3.8 14.6 - - - +
141B VAL* 1.3 76.8 - - - +
143B ALA* 1.3 58.5 + - - +
145B LEU* 3.4 4.5 + - - +
146B LYS* 2.9 34.0 + - + +
158B GLU* 2.7 35.1 + - - -
161B HIS* 5.2 9.4 + - + -
162B ASP* 3.1 29.2 + - - +
165B VAL* 4.0 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS 5.2 4.7 - - - +
130B LEU* 4.4 20.0 - - + -
139B ASP 2.9 18.5 + - - +
140B GLU 3.7 4.3 - - - +
142B LYS* 1.3 78.6 - - - +
144B TYR* 1.3 61.5 + - - +
146B LYS* 3.4 10.9 + - - +
147B LYS* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.0 20.9 + - - -
152A HIS* 3.2 26.1 - + - -
204A 1PE 4.0 17.3 - - - -
124B SER 5.0 0.2 - - - -
127B GLU* 2.7 40.1 + - + -
128B MET* 3.6 42.8 - - + -
130B LEU* 6.3 0.7 - - + -
140B GLU 3.1 13.9 + - - +
141B VAL* 3.3 9.8 + - - +
143B ALA* 1.3 74.1 - - - +
145B LEU* 1.3 59.7 + - - +
147B LYS* 3.4 30.4 + - - +
148B GLU* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 4.3 9.2 - - + -
204A 1PE 3.6 39.7 - - - +
141B VAL* 3.0 23.7 + - + +
142B LYS* 3.7 4.3 - - - +
144B TYR* 1.3 76.6 - - - +
146B LYS* 1.3 62.6 + - - +
148B GLU* 3.9 3.3 - - - +
149B PHE* 3.0 35.0 + - + +
161B HIS* 3.7 18.3 - - + +
164B LEU* 3.8 32.5 - - + -
165B VAL* 3.6 30.5 - - + -
168B ILE* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 2.9 23.3 + - + +
143B ALA* 3.5 9.2 - - - +
145B LEU* 1.3 79.2 - - - +
147B LYS* 1.3 58.7 + - + +
149B PHE* 3.8 2.1 - - - +
150B GLU* 2.4 72.5 + - - +
156B VAL* 3.8 23.5 - - + +
161B HIS* 4.4 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.7 53.9 - - + +
22A LYS 4.4 8.2 + - - +
24A LYS* 3.8 19.8 - - - +
27A ASP* 5.0 0.4 + - - -
117A ASN* 4.5 0.5 - - - +
143B ALA 3.1 14.7 + - - +
144B TYR* 3.5 37.5 - - - +
146B LYS* 1.3 77.1 - - + +
148B GLU* 1.3 89.0 + - - +
150B GLU* 3.7 11.7 - - - +
151B LYS* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.0 25.6 + - - -
148A GLU* 5.3 1.9 - - - +
152A HIS* 4.9 1.2 + - - -
204A 1PE 3.7 30.5 - - - +
144B TYR* 2.9 39.7 + - + +
145B LEU 3.9 2.5 - - - +
147B LYS* 1.3 107.2 + - - +
149B PHE* 1.3 60.6 + - - +
151B LYS* 2.9 33.9 + - - +
152B HIS* 3.0 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.3 11.7 - - + -
149A PHE* 4.2 12.8 - + - -
164A LEU* 3.9 41.1 - - + -
167A ASP* 5.9 0.2 - - - -
168A ILE* 4.3 15.3 - - + -
204A 1PE 3.9 25.8 - - - -
145B LEU* 3.0 26.4 + - + +
146B LYS 3.8 3.1 - - - +
148B GLU* 1.3 76.3 - - + +
150B GLU* 1.3 64.1 + - - +
152B HIS* 3.0 8.8 + - - +
154B ALA* 2.9 49.3 + - + +
155B VAL 3.9 11.0 - - - -
156B VAL* 3.8 7.4 - - + -
161B HIS* 3.7 24.0 - + - -
164B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.4 17.1 + - - +
188A LYS* 4.7 2.3 + - - +
190A ASP* 4.9 9.6 - - - +
146B LYS* 2.4 61.1 + - - +
147B LYS* 3.3 10.2 + - - +
149B PHE* 1.3 77.1 - - - +
151B LYS* 1.3 63.3 + - - +
153B GLY* 3.0 15.2 + - - +
154B ALA 4.0 6.5 - - - +
155B VAL* 6.1 0.2 - - - -
156B VAL* 4.1 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.7 15.3 - - - +
24A LYS* 4.0 16.6 - - - +
25A GLY 4.8 6.7 + - - -
26A GLY 6.3 0.7 - - - -
27A ASP* 3.9 11.6 + - - +
117A ASN* 3.4 28.2 - - + +
118A GLY 4.0 9.3 - - - +
188A LYS* 3.0 27.5 + - - -
147B LYS* 2.8 23.5 + - - +
148B GLU* 2.9 47.5 + - - +
150B GLU* 1.3 76.9 - - - +
152B HIS* 1.3 71.1 + - + +
153B GLY 3.1 0.2 - - - -
203B PGO 4.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 2.8 38.8 + - - -
144A TYR* 3.6 25.7 + + - -
148A GLU* 6.1 0.2 - - - +
188A LYS* 4.4 1.3 - - - -
204A 1PE 3.5 49.0 + - - +
148B GLU* 3.0 26.9 + - - -
149B PHE 3.0 5.3 + - - +
151B LYS* 1.3 95.4 + - + +
153B GLY* 1.3 52.0 + - - +
154B ALA* 3.4 0.3 + - - -
203B PGO 2.7 51.8 + - + +
----------------------------------------------------------
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