Contacts of the helix formed by residues 116 - 131 (chain A) in PDB entry 2CXF
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 TYR 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.3 5.2 - - + -
104A SER* 3.3 37.2 + - - -
108A LEU* 4.4 19.1 - - + +
112A LEU* 3.9 40.6 - - + -
113A ASP* 3.3 17.2 + - - +
114A SER 3.5 0.6 - - - -
115A ASP* 1.3 75.9 - - - +
117A ALA* 1.3 67.1 + - - +
118A PRO* 3.4 40.1 - - + +
119A LEU* 2.9 22.8 + - + +
120A GLN* 3.1 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP 3.5 5.7 + - - -
116A TYR* 1.3 70.8 - - - +
118A PRO* 1.3 66.9 - - + +
120A GLN* 3.2 13.7 + - - +
121A GLN* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER* 5.5 0.7 - - - +
101A LEU* 3.5 19.6 - - + +
104A SER* 4.7 11.2 - - - +
116A TYR* 3.4 44.0 - - + +
117A ALA* 1.3 94.6 - - + +
119A LEU* 1.3 62.1 + - - +
121A GLN* 3.3 16.5 + - + +
122A PHE* 3.1 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.5 26.3 - - + +
112A LEU* 4.4 19.5 - - + -
113A ASP 3.1 27.1 - - - +
114A SER* 4.8 0.7 - - - -
116A TYR* 2.9 21.0 + - + +
118A PRO* 1.3 79.5 - - - +
120A GLN* 1.3 64.4 + - + +
122A PHE* 2.9 22.5 + - + +
123A PHE* 3.4 15.7 + - + -
189A LEU* 4.7 14.4 - - + -
236A ILE* 5.3 2.2 - - + -
238A ALA* 4.4 4.0 - - + -
240A PHE* 3.4 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.0 33.1 + - - +
115A ASP* 4.4 4.3 - - - +
116A TYR 3.1 8.6 + - - +
117A ALA* 3.7 20.5 + - - +
119A LEU* 1.3 78.2 - - + +
121A GLN* 1.3 62.5 + - - +
123A PHE* 3.5 15.3 + - + +
124A VAL* 3.3 25.4 + - + +
186A ARG* 5.4 8.5 - - - +
240A PHE* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 5.4 2.6 + - - +
97A SER* 4.5 22.0 + - - +
117A ALA 2.8 14.2 + - - +
118A PRO* 3.3 18.5 + - + +
120A GLN* 1.3 78.2 - - - +
122A PHE* 1.3 65.5 + - - +
124A VAL* 3.3 10.1 + - - +
125A VAL* 3.3 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 6.3 1.8 - - + -
97A SER* 4.0 27.6 - - - +
98A ILE* 3.9 11.0 - - + -
101A LEU* 3.7 28.3 - - + -
118A PRO 3.1 4.6 + - - +
119A LEU* 2.9 11.2 + - + +
121A GLN* 1.3 78.3 - - - +
123A PHE* 1.3 99.6 + + - +
125A VAL* 3.1 7.2 + - + +
126A MSE 2.9 41.7 + - + +
189A LEU* 4.1 5.4 - - + -
194A LEU* 4.0 16.8 - - + -
230A LEU* 3.7 17.9 - - + -
233A LEU* 3.4 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.4 15.8 + - + -
120A GLN* 3.8 11.4 - - + +
121A GLN 3.4 0.2 - - - -
122A PHE* 1.3 105.8 - + - +
124A VAL* 1.3 65.9 + - + +
126A MSE 2.8 9.6 + - + +
127A GLU* 2.7 25.3 + - - +
182A ARG* 6.4 1.1 - - + -
185A LEU* 4.5 26.7 - - + +
186A ARG* 3.3 48.9 - - + +
189A LEU* 4.2 13.9 - - + -
194A LEU* 5.6 0.2 - - + -
240A PHE* 3.3 43.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 3.3 17.9 - - + +
121A GLN* 3.3 9.4 + - + +
123A PHE* 1.3 78.5 - - + +
125A VAL* 1.3 61.3 + - + +
127A GLU* 3.2 9.0 + - - +
128A HIS* 2.6 51.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MSE 3.5 36.3 - - + +
94A ALA* 3.7 27.8 - - + +
97A SER* 3.2 27.6 - - - +
121A GLN* 3.4 21.5 - - + +
122A PHE* 3.1 6.5 + - + +
123A PHE 3.1 0.4 - - - -
124A VAL* 1.3 77.2 - - + +
126A MSE 1.3 65.8 + - - +
128A HIS* 3.1 12.5 + - - +
129A CYS* 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 5.8 2.0 - - + -
122A PHE* 2.9 41.5 + - + +
123A PHE* 2.8 19.3 + - - +
125A VAL* 1.3 72.3 - - - +
127A GLU* 1.3 62.1 + - - +
129A CYS* 3.0 40.4 + - + +
130A LEU* 3.0 35.5 + - + +
185A LEU* 4.5 22.0 - - + -
194A LEU* 5.4 4.3 - - + -
198A MSE 5.6 6.7 - - - +
218A MSE 5.8 2.9 - - - -
226A ILE* 4.5 16.8 - - + -
230A LEU* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE 2.7 13.8 + - - +
124A VAL* 3.4 13.5 - - - +
126A MSE 1.3 73.1 - - - +
128A HIS* 1.3 64.5 + - - +
130A LEU* 3.1 10.6 + - - +
131A LYS* 2.9 55.7 + - + +
147A PHE* 3.3 29.2 - - + -
178A VAL* 4.0 0.2 - - - +
182A ARG* 2.6 56.3 + - - +
185A LEU* 5.1 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.5 29.0 - - + +
93A MSE 4.4 10.3 - - + +
124A VAL* 2.6 44.9 + - + -
125A VAL* 3.1 7.9 + - - +
127A GLU* 1.3 85.8 - - + +
129A CYS* 1.3 61.6 + - - +
131A LYS* 3.5 12.9 + - + +
132A HIS* 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.0 21.1 - - - -
94A ALA* 4.4 12.1 - - - -
125A VAL* 3.0 38.3 + - - -
126A MSE 3.0 28.4 + - + +
128A HIS* 1.3 79.4 - - - +
130A LEU* 1.3 60.8 + - + +
131A LYS 3.2 1.0 + - - -
132A HIS 3.6 8.8 + - - +
217A LEU* 3.6 39.3 - - + +
218A MSE 4.3 6.5 - - - +
226A ILE* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A MSE 3.0 30.6 + - + +
127A GLU* 3.1 8.0 + - - +
129A CYS* 1.3 77.2 - - - +
131A LYS* 1.3 57.7 + - - +
132A HIS 3.4 0.2 - - - -
134A LEU* 3.5 4.3 - - - +
147A PHE* 3.5 33.7 - - + +
151A LEU* 4.3 18.2 - - + -
185A LEU* 4.1 29.2 - - + -
198A MSE 4.5 11.0 - - - -
212A TYR* 2.7 33.5 + - - +
218A MSE 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 2.9 56.1 + - + +
128A HIS* 4.0 13.4 - - + +
129A CYS 3.2 0.6 - - - -
130A LEU* 1.3 77.9 - - - +
132A HIS* 1.3 59.6 + - - +
133A GLY 3.4 6.1 + - - -
134A LEU* 3.6 22.0 + - + +
146A SER* 4.0 13.0 - - - +
147A PHE* 3.8 21.8 - - + -
178A VAL* 4.7 8.9 - - - +
182A ARG* 4.7 3.0 - - - +
----------------------------------------------------------
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