Contacts of the helix formed by residues 116 - 129 (chain D) in PDB entry 6C3P
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 116 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 3.6 8.0 - - - +
91D TRP* 4.2 8.6 - - - +
100D LEU* 4.4 0.2 - - - +
114D ILE* 4.9 1.7 - - - +
115D HIS* 1.3 79.6 + - - +
117D PHE* 1.3 57.9 + - - +
118D SER* 3.3 14.2 - - - -
119D SER* 2.7 45.2 + - - -
120D ALA* 3.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 4.3 22.4 - - + -
87D ALA* 3.7 18.8 - - + -
88D MET* 3.6 44.0 - - + -
91D TRP* 3.7 47.3 - + + +
116D SER* 1.3 73.0 - - - +
118D SER* 1.3 63.4 + - - +
120D ALA 3.2 1.5 + - - +
121D PHE* 2.9 26.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 3.2 21.6 + - - +
146A ILE* 3.3 26.7 - - - +
116D SER* 3.0 13.1 + - - -
117D PHE* 1.3 81.1 - - - +
119D SER* 1.3 56.1 + - - +
121D PHE* 3.2 8.0 + - - +
122D LEU* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 2.4 35.5 + - - -
113D SER 4.6 1.8 + - - -
114D ILE* 3.5 30.0 - - - -
115D HIS* 3.4 12.4 + - - +
116D SER* 2.7 28.6 + - - -
118D SER* 1.3 72.1 - - - +
120D ALA* 1.3 55.0 + - - -
121D PHE 3.2 0.2 + - - -
122D LEU* 3.3 5.6 + - - +
123D PHE* 2.9 28.4 + - - +
136D ARG* 3.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ALA* 3.5 22.9 - - - +
90D TRP* 4.1 6.8 - - + -
91D TRP* 3.5 29.4 - - + +
114D ILE* 4.4 11.3 - - + +
116D SER 3.2 5.8 + - - +
117D PHE 3.2 5.1 + - - +
119D SER* 1.3 77.3 - - - +
121D PHE* 1.3 56.5 + - - +
123D PHE* 3.3 8.9 + - - +
124D SER* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.0 18.8 - - + -
150A ILE* 3.6 25.6 - - + -
80D LEU* 4.6 7.0 - - + -
83D TRP* 3.9 22.2 - + + -
84D LEU* 3.6 33.7 - - + -
87D ALA* 3.6 24.7 - - + +
117D PHE* 2.9 23.3 + + + +
118D SER* 3.6 7.6 - - - +
120D ALA* 1.3 74.7 - - - +
122D LEU* 1.3 67.0 + - - +
124D SER* 3.1 2.9 + - - -
125D ILE* 3.0 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.9 42.0 - - + +
139A THR 4.1 15.9 - - - +
140A GLU* 3.9 23.8 - - + +
146A ILE* 4.0 21.5 - - + -
149A LEU* 4.1 17.9 - - + +
118D SER* 2.9 19.1 + - - +
119D SER 3.6 6.5 - - - +
121D PHE* 1.3 75.3 - - - +
123D PHE* 1.3 57.9 + - - +
125D ILE* 3.3 7.7 + - + +
126D GLU* 2.9 35.9 + - + +
136D ARG* 4.2 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PHE* 3.8 14.8 - + - -
90D TRP* 3.3 53.2 - + + -
111D VAL* 3.6 20.9 - - + -
114D ILE* 4.9 3.6 - - + -
119D SER 2.9 17.2 + - - +
120D ALA* 3.5 7.0 - - - +
121D PHE 3.1 0.2 - - - -
122D LEU* 1.3 76.6 - - - +
124D SER* 1.3 57.5 + - - +
126D GLU* 3.2 7.6 + - - +
127D VAL* 2.9 50.2 + - + +
136D ARG* 3.3 43.7 - - + +
137D MET* 4.3 0.2 - - - -
138D VAL* 3.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D TRP* 3.6 25.1 - - - -
86D PHE 3.3 0.2 - - - -
87D ALA* 3.0 27.9 + - - -
90D TRP* 3.1 14.6 - - - -
120D ALA 2.9 11.8 + - - -
121D PHE 3.1 4.5 + - - -
123D PHE* 1.3 75.7 - - - +
125D ILE* 1.3 58.2 + - - +
127D VAL* 3.3 0.6 + - - -
128D GLN* 2.9 28.2 + - - +
152D GLN* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 5.1 2.2 - - + -
149A LEU* 4.1 18.8 - - + -
150A ILE* 3.8 19.1 - - + -
153A ASN* 3.5 28.0 - - - +
83D TRP* 3.9 24.7 - - + -
121D PHE* 3.0 52.4 + - + +
122D LEU* 3.7 8.1 - - - +
123D PHE 3.2 0.2 - - - -
124D SER* 1.3 77.3 - - - +
126D GLU* 1.3 63.2 + - + +
129D VAL* 3.0 40.8 + - + +
131D ILE* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 5.9 0.5 - - - +
149A LEU* 6.0 3.8 - - + -
131C ILE* 4.8 0.2 - - - +
133C PHE* 4.4 1.2 - - + -
122D LEU* 2.9 22.4 + - + +
123D PHE* 3.2 6.5 + - - +
125D ILE* 1.3 76.7 - - + +
127D VAL* 1.3 62.5 + - + +
130D THR* 3.2 1.4 + - - -
131D ILE* 2.7 35.0 + - + -
132D GLY* 3.2 18.3 + - - +
133D PHE* 3.0 50.4 + - + +
134D GLY 4.5 0.3 + - - -
136D ARG* 2.7 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ILE* 4.0 14.3 - - + +
133C PHE* 4.1 11.0 - - + -
123D PHE* 2.9 55.0 + - + +
124D SER* 3.7 4.0 - - - +
126D GLU* 1.3 75.7 - - - +
128D GLN* 1.3 61.4 + - - +
130D THR* 2.8 24.4 + - - +
149D LEU* 3.6 27.1 - - + -
152D GLN* 4.0 20.6 - - + +
153D ASN* 3.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PHE* 4.8 4.9 - - - -
82D SER* 2.7 36.7 + - - +
83D TRP* 2.9 31.2 - - - +
86D PHE* 5.2 0.4 - - - -
124D SER 2.9 10.6 + - - +
127D VAL* 1.3 80.6 - - - +
129D VAL* 1.3 59.9 + - - +
130D THR* 3.4 8.3 + - - +
152D GLN* 3.3 31.6 + - + +
153D ASN* 5.2 2.5 - - - +
156D GLY* 3.7 34.4 - - - +
159D ILE* 3.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 3.5 19.8 - - + +
153A ASN* 3.7 25.1 - - + +
157A LEU* 5.3 14.6 - - + -
83D TRP* 3.4 37.5 - - + +
125D ILE* 3.0 26.4 + - + +
128D GLN* 1.3 75.5 - - - +
130D THR* 1.3 75.3 + - - +
131D ILE* 3.7 15.3 - - + -
----------------------------------------------------------
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