Contacts of the helix formed by residues 128 - 141 (chain D) in PDB entry 1JPL
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 GLU 128 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 4.3 10.0 + - - +
81D HIS 4.1 12.4 - - - +
82D ASN* 3.5 23.5 - - - +
85D GLY* 3.4 21.8 - - - +
125D LEU* 3.1 34.0 + - + +
126D PRO 4.4 1.3 - - - -
127D GLU* 1.3 80.8 - - + +
129D ALA* 1.3 63.7 + - - +
130D LYS 3.4 2.2 - - - -
131D ILE* 3.4 40.6 + - + +
132D LYS* 3.8 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D PRO 5.2 2.5 - - - +
127D GLU 3.2 9.5 + - - +
128D GLU* 1.3 70.3 - - - +
130D LYS* 1.3 62.8 + - + +
132D LYS* 3.1 13.8 + - - +
133D ASP* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLY 3.4 26.6 + - - +
86D LYS* 4.8 4.9 - - - +
87D PHE* 3.4 46.8 - - + +
90D LEU* 3.3 8.5 - - + +
128D GLU 3.4 1.2 - - - -
129D ALA* 1.3 75.5 - - + +
131D ILE* 1.3 65.8 + - - +
133D ASP* 4.1 4.0 - - - +
134D ALA* 2.9 25.8 + - - +
304H ASP* 3.7 26.6 + - - +
306H ASP* 2.8 34.5 + - - +
307H GLU 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL* 4.4 11.2 - - + -
85D GLY* 3.9 19.1 - - - -
90D LEU* 3.7 14.6 - - + -
118D LEU* 3.7 26.4 - - + +
121D TRP* 3.7 35.7 - - + +
122D THR* 4.1 7.4 - - + +
125D LEU* 4.1 12.8 - - + -
128D GLU* 3.4 35.6 + - + +
129D ALA 3.2 0.8 - - - -
130D LYS* 1.3 77.1 - - - +
132D LYS* 1.3 58.8 + - - +
134D ALA* 3.7 2.0 - - - +
135D TYR* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D THR* 2.8 49.2 + - - -
125D LEU 4.1 1.6 + - - -
126D PRO* 3.1 39.1 + - - +
128D GLU 4.1 8.3 - - - +
129D ALA* 3.1 11.5 + - - +
131D ILE* 1.3 76.4 - - - +
133D ASP* 1.3 58.8 + - - +
135D TYR* 3.1 0.3 + - - +
136D HIS* 2.7 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 4.1 22.5 - - + -
129D ALA* 2.9 25.4 + - - +
130D LYS* 3.4 8.3 + - - +
132D LYS* 1.3 77.4 - - - +
134D ALA* 1.3 62.0 + - - +
136D HIS* 4.2 6.8 - - - +
137D MSE 3.2 23.9 + - - +
140D ARG* 4.8 2.9 + - - +
309H LEU* 3.9 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 4.6 0.4 - - - -
90D LEU* 4.1 23.8 - - + -
94D ILE* 5.0 9.3 - - + +
118D LEU* 5.0 4.5 - - + -
130D LYS 2.9 18.4 + - - +
131D ILE 3.7 3.8 - - - +
133D ASP* 1.3 76.2 - - - +
135D TYR* 1.3 65.7 + - - +
137D MSE 3.2 4.9 + - - +
138D LEU* 3.2 28.3 + - + +
309H LEU* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.3 16.6 - - + -
118D LEU* 3.9 22.8 - - + +
119D TYR* 3.3 36.6 - + + -
122D THR* 3.7 22.4 - - + -
131D ILE 2.9 18.4 + - - +
132D LYS 3.1 1.8 + - - +
134D ALA* 1.3 77.1 - - - +
136D HIS* 1.3 73.6 - + - +
138D LEU* 3.3 23.9 + - + +
139D LYS* 3.4 29.8 + - + +
144D VAL* 3.8 12.3 - - + +
147D ASP* 2.8 38.7 + - - -
148D PRO* 3.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D THR* 5.7 3.1 - - + -
132D LYS* 2.7 56.0 + - + +
133D ASP* 4.2 7.2 - - - +
135D TYR* 1.3 87.6 - + - +
137D MSE 1.3 62.8 + - - +
139D LYS* 3.2 14.5 + - - +
140D ARG* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE* 4.8 3.4 - - + -
133D ASP 3.2 19.6 + - - +
134D ALA 3.5 4.9 - - - +
135D TYR 3.2 0.2 - - - -
136D HIS* 1.3 78.6 - - - +
138D LEU* 1.3 75.5 + - + +
140D ARG* 3.0 29.7 + - - +
141D GLN* 2.9 67.7 + - + +
309H LEU* 4.2 15.5 - - + -
310H LEU 3.5 24.5 - - - +
311H HIS* 4.4 8.7 - - + -
312H ILE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE* 4.2 22.7 - - + +
97D VAL* 4.1 22.9 - - + -
98D SER* 5.9 0.2 - - - -
114D VAL* 6.3 0.4 - - + -
115D ILE* 4.1 22.0 - - + -
118D LEU* 4.9 14.1 - - + -
134D ALA* 3.2 16.1 + - + +
135D TYR* 3.3 15.2 + - + +
137D MSE 1.3 95.2 - - + +
139D LYS* 1.3 59.3 + - - +
141D GLN* 3.8 0.8 + - - -
142D GLY 3.4 1.4 + - - -
143D ILE* 2.9 41.7 + - + +
144D VAL* 3.0 18.5 + - + -
312H ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D TYR* 3.4 36.3 - - + +
136D HIS* 3.2 15.2 + - - +
137D MSE 3.0 0.6 - - - -
138D LEU* 1.3 77.4 - - - +
140D ARG* 1.3 64.0 + - + +
141D GLN 3.2 0.2 - - - -
142D GLY* 3.3 11.6 + - - -
144D VAL* 3.5 31.5 - - + +
145D GLN 5.2 1.6 - - - -
146D SER* 4.8 5.1 - - - +
147D ASP* 2.8 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ASP* 4.8 3.0 + - - +
136D HIS* 3.0 36.3 + - + +
137D MSE 3.0 33.0 + - + +
139D LYS* 1.3 78.8 - - + +
141D GLN* 1.3 64.5 + - + +
142D GLY 3.5 0.2 + - - -
309H LEU* 5.5 2.8 - - - +
311H HIS* 5.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D MSE 2.9 45.8 + - + +
138D LEU 4.2 4.3 - - - +
140D ARG* 1.3 81.0 + - + +
142D GLY* 1.3 60.2 + - - +
143D ILE* 3.3 14.3 + - + +
311H HIS* 5.4 2.3 - - - +
312H ILE* 2.7 36.8 + - + +
----------------------------------------------------------
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