Contacts of the helix formed by residues 137 - 150 (chain D) in PDB entry 3PJV
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 PRO 137 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 4.4 10.5 - - + -
134D VAL* 6.1 0.2 - - + -
135D SER 3.5 4.3 - - - +
136D HIS* 1.3 93.6 - - + +
138D MSE 1.3 57.0 + - - +
139D PHE 3.2 2.7 - - - -
140D ALA* 3.1 4.8 + - + +
141D LEU* 2.8 42.2 + - + +
38F LEU* 4.3 24.5 - - + -
77F SER* 3.5 12.8 - - - +
98F ALA* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 5.5 0.7 - - - +
136D HIS* 3.1 40.9 + - + +
137D PRO* 1.3 76.6 - - - +
139D PHE* 1.3 61.3 + - + +
141D LEU* 3.6 2.9 + - - +
142D ALA* 3.0 27.0 + - - +
96F ILE* 3.3 28.9 - - + -
97F PRO 3.8 6.7 - - - +
98F ALA 3.4 15.9 - - - +
99F VAL* 5.0 3.8 - - - -
100F THR* 4.9 10.3 - - + +
138F MSE 3.6 32.3 - - + +
139F PHE* 3.7 32.3 - - + -
142F ALA* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D SER 3.9 17.3 - - - +
74D GLY* 3.2 24.2 - - - +
75D TYR* 3.5 22.7 - + + -
136D HIS* 4.7 6.9 + - + +
137D PRO 3.2 0.6 - - - -
138D MSE 1.3 77.0 - - + +
140D ALA* 1.3 67.3 + - - +
142D ALA* 3.3 3.4 + - - +
143D LYS* 3.0 29.4 + - - +
75F TYR* 3.5 40.2 - + + -
136F HIS* 4.0 20.2 - + + -
138F MSE 3.2 39.0 - - + -
139F PHE* 3.8 23.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D SER 4.9 2.8 + - - +
112D LEU* 4.2 15.3 - - + -
136D HIS 5.5 0.2 + - - -
137D PRO* 3.1 11.5 + - + +
139D PHE* 1.3 78.8 - - - +
141D LEU* 1.3 62.5 + - - +
143D LYS* 3.2 8.6 + - - +
144D LEU* 3.0 28.6 + - - +
34F TYR* 3.9 30.4 - - + -
37F GLN* 5.7 2.5 - - - +
38F LEU* 4.3 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 3.9 14.2 - - + +
106D PHE* 4.2 8.9 - - + -
107D VAL* 4.2 23.1 - - + -
110D ILE* 4.1 27.1 - - + -
112D LEU* 4.4 13.0 - - + -
137D PRO* 2.8 33.6 + - + +
138D MSE 3.9 4.3 - - - +
140D ALA* 1.3 73.7 - - - +
142D ALA* 1.3 62.4 + - - +
144D LEU* 3.3 6.7 + - + +
145D TRP* 2.9 25.6 + - - +
98F ALA* 3.8 36.3 - - + +
99F VAL* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D THR* 3.9 24.5 - - - +
102D VAL* 3.8 13.4 - - + +
138D MSE 3.0 18.3 + - - +
139D PHE* 3.6 6.3 - - - +
140D ALA 3.3 0.4 - - - -
141D LEU* 1.3 77.1 - - - +
143D LYS* 1.3 58.2 + - + +
145D TRP* 3.4 2.1 + - - +
146D GLN* 3.0 38.8 + - - +
138F MSE 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.9 0.6 + - - -
72D ASP* 2.8 35.0 + - - +
73D SER 4.3 2.3 + - - +
74D GLY* 3.9 21.7 - - - +
139D PHE 3.0 23.9 + - - +
140D ALA* 3.2 6.9 + - - +
142D ALA* 1.3 75.0 - - + +
144D LEU* 1.3 63.6 + - - +
146D GLN* 3.4 18.1 + - - +
147D SER* 3.0 26.3 + - - -
33F GLN* 4.9 1.6 - - - +
34F TYR* 3.5 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PHE* 3.9 15.7 - - + -
110D ILE* 4.1 28.7 - - + -
112D LEU* 4.3 17.9 - - + -
140D ALA 3.0 22.6 + - - +
141D LEU* 3.7 7.4 - - + +
143D LYS* 1.3 74.9 - - - +
145D TRP* 1.3 58.2 + - - +
147D SER* 3.3 6.5 + - - -
148D ALA* 2.9 27.0 + - - +
27F LEU* 4.2 21.9 - - + +
30F SER* 4.1 17.3 - - - -
31F ARG* 4.4 11.4 - - + +
34F TYR* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D THR* 3.5 25.7 - - + +
101D ASN 4.4 5.0 + - - -
102D VAL* 3.8 12.6 - - + -
103D PRO* 3.6 37.2 - - + +
105D TRP* 3.8 21.1 - + - -
106D PHE* 3.5 44.1 - + + -
141D LEU 2.9 17.2 + - - +
142D ALA 3.6 2.9 - - - +
144D LEU* 1.3 73.4 - - - +
146D GLN* 1.3 66.1 + - + +
148D ALA* 3.0 8.2 + - + +
149D LEU* 2.9 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLY* 5.9 0.5 - - - -
96D ILE* 2.9 39.4 + - + +
100D THR* 3.1 27.5 + - + +
142D ALA* 3.0 28.6 + - - +
143D LYS* 3.7 17.0 - - - +
145D TRP* 1.3 75.5 - - + +
147D SER* 1.3 61.5 + - - +
149D LEU* 3.3 14.4 + - + +
150D GLY* 3.3 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LYS 3.0 14.3 + - - -
144D LEU* 3.5 10.3 - - - -
146D GLN* 1.3 76.1 - - - +
148D ALA* 1.3 61.9 + - - +
150D GLY* 3.2 19.4 + - - +
27F LEU* 3.7 25.3 - - - +
30F SER* 5.0 3.5 + - - -
34F TYR* 4.7 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PHE* 3.9 24.7 - - + -
144D LEU 2.9 13.6 + - - +
145D TRP* 3.0 15.9 + - + +
147D SER* 1.3 77.2 - - - +
149D LEU* 1.3 59.7 + - - +
150D GLY 3.4 6.8 + - - +
24F MSE 5.0 8.7 - - + +
27F LEU* 4.5 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D TRP* 2.9 66.0 + - + +
146D GLN* 3.7 13.7 - - + +
147D SER 3.3 0.2 - - - -
148D ALA* 1.3 76.3 - - - +
150D GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN 3.3 8.5 + - - -
147D SER* 3.2 16.0 + - - +
148D ALA 3.1 8.3 - - - +
149D LEU* 1.3 81.9 - - - +
----------------------------------------------------------
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