Contacts of the helix formed by residues 117 - 129 (chain A) in PDB entry 5PM6
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 ASN 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 3.5 14.2 - - - -
116A GLN* 1.3 88.9 - - - +
118A PHE* 1.3 66.3 + - - +
119A GLU* 3.2 12.4 + - - +
120A ASP* 2.9 33.5 + - - +
121A LEU 3.1 15.4 + - - -
123A ARG* 4.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 5.5 6.3 - + - -
117A ASN* 1.3 77.2 - - - +
119A GLU* 1.3 56.9 + - - +
121A LEU* 3.3 7.1 + - - +
122A GLU* 2.9 29.5 + - - +
209A PRO* 4.0 22.2 - - + -
265A THR* 3.6 26.9 - - + -
267A GLU* 4.0 31.6 - - + -
283A PHE* 5.8 0.3 - - - -
285A HIS* 3.8 21.1 - + + -
409A EDO 3.1 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.2 11.3 + - - +
118A PHE* 1.3 76.4 - - - +
120A ASP* 1.3 63.7 + - - +
122A GLU* 3.4 17.3 + - - +
123A ARG* 3.0 49.2 + - + +
409A EDO 4.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 3.3 9.5 - - - -
116A GLN* 2.9 36.6 + - + +
117A ASN* 2.9 23.6 + - - +
119A GLU* 1.3 74.1 - - - +
121A LEU* 1.3 57.6 + - - +
123A ARG* 3.3 28.5 + - - +
124A LYS* 3.0 52.1 + - - +
415A SO4 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 3.9 14.1 - - + -
113A PRO* 4.1 12.3 - - + -
115A HIS* 3.8 38.8 - - + +
117A ASN 3.1 13.0 + - - +
118A PHE* 3.7 9.2 - - + +
119A GLU 3.2 0.2 - - - -
120A ASP* 1.3 80.0 - - - +
122A GLU* 1.3 55.5 + - - +
124A LYS* 3.2 5.9 + - + +
125A TYR* 2.9 28.3 + - - +
185A TRP* 3.5 34.7 - - + -
283A PHE* 5.0 1.8 - - + -
285A HIS* 3.5 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE 2.9 17.4 + - - +
119A GLU* 3.6 13.3 - - - +
121A LEU* 1.3 73.2 - - - +
123A ARG* 1.3 64.9 + - - +
125A TYR* 3.3 1.2 + - - +
126A TRP* 3.1 31.1 + - + -
213A TYR* 2.5 33.0 + - - +
251A PRO* 4.2 0.5 - - - +
263A ARG* 2.8 34.8 + - - -
283A PHE* 4.0 18.5 - - + -
406A EDO 4.3 6.7 + - - -
409A EDO 3.7 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 4.8 3.2 + - - +
119A GLU* 3.0 40.0 + - + +
120A ASP* 3.3 44.3 + - - +
122A GLU* 1.3 76.0 - - - +
124A LYS* 1.3 60.2 + - + +
126A TRP* 3.4 2.9 + - - +
127A LYS* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 4.1 18.1 - - + +
114A PRO 3.4 26.7 + - - +
115A HIS* 4.2 5.2 - - + -
120A ASP* 3.0 41.8 + - - +
121A LEU* 3.2 9.2 + - - +
123A ARG* 1.3 79.6 - - + +
125A TYR* 1.3 55.4 + - - +
127A LYS* 4.4 3.1 - - - -
128A ASN* 2.9 44.4 + - - +
185A TRP* 4.4 11.4 - - + -
186A LYS* 4.7 0.7 - - - -
415A SO4 2.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.1 4.2 - - - -
121A LEU 2.9 13.4 + - - +
122A GLU 3.6 7.0 - - - +
123A ARG 3.3 0.2 - - - -
124A LYS* 1.3 76.3 - - - +
126A TRP* 1.3 103.8 + + - +
129A ARG* 2.8 65.7 + - + +
185A TRP* 3.8 13.8 - + + -
186A LYS* 3.7 21.3 - - + +
188A THR* 2.7 34.4 + - - +
282A GLY 4.6 1.0 + - - -
283A PHE* 3.4 49.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.7 37.9 - - - +
84A GLY* 5.0 0.7 - - - -
86A PHE* 3.9 22.7 - + - -
122A GLU* 3.1 29.9 + - + +
123A ARG* 4.3 2.5 - - - +
125A TYR* 1.3 102.5 - + - +
127A LYS* 1.3 63.4 + - - +
129A ARG* 4.5 2.5 + - + +
130A ILE 5.7 0.2 + - - -
191A TRP* 5.6 0.2 - - - -
213A TYR* 2.9 43.5 + + - -
248A LEU* 4.3 18.2 - - + -
249A ILE 3.8 10.8 - - - -
250A SER* 3.5 36.6 - - - -
251A PRO* 3.4 24.9 - - + +
281A ALA* 6.2 1.3 - - + -
282A GLY* 6.1 1.3 - - - -
283A PHE* 4.3 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.2 10.3 - - - +
123A ARG 2.9 21.9 + - - +
124A LYS* 3.8 3.8 - - - +
126A TRP* 1.3 80.9 - - - +
128A ASN* 1.3 73.7 + - - +
130A ILE* 5.2 0.6 - - - +
131A TYR* 3.7 16.5 - - - -
415A SO4 3.0 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 2.9 26.6 + - - +
127A LYS* 1.3 100.6 + - - +
129A ARG* 1.3 65.8 + - - +
130A ILE 3.1 4.0 + - - -
131A TYR* 3.1 23.9 + - + -
132A ASN* 3.3 5.2 - - - +
186A LYS* 3.2 23.8 + - - +
415A SO4 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 2.9 30.6 + - - +
79A ALA* 4.0 14.7 - - - +
83A ALA 5.8 0.4 - - - +
86A PHE* 3.6 28.7 - - + -
88A GLN* 2.9 29.5 + - - +
125A TYR* 2.8 42.6 + - + +
126A TRP* 4.5 3.0 + - - +
127A LYS 3.8 0.8 - - - -
128A ASN* 1.3 72.5 - - - +
130A ILE* 1.3 63.3 + - - +
131A TYR 3.1 1.6 + - - -
132A ASN* 2.8 38.7 + - - +
134A PRO* 3.7 8.6 - - - +
186A LYS* 3.6 27.1 + - - +
188A THR* 3.0 23.9 + - - -
----------------------------------------------------------
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