Contacts of the helix formed by residues 118 - 136 (chain A) in PDB entry 2D2C
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 TRP 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 5.7 0.2 - - - +
104A VAL* 3.7 10.6 - - + +
105A TYR* 5.4 2.0 - + - +
109A GLY 3.8 9.2 - - - +
110A PHE* 3.4 34.5 - + + +
114A ARG 3.8 3.3 + - - +
115A GLU 5.4 0.4 - - - -
116A LEU 2.5 5.5 + - - +
117A THR* 1.3 75.0 + - - +
119A ILE* 1.3 83.5 + - + +
121A GLY* 2.8 6.6 + - - -
122A VAL* 2.7 41.6 + - + -
302A HEM 3.1 64.8 - - + +
108B LEU* 3.1 46.7 - - + -
109B ILE* 3.7 11.7 - - - -
111B VAL* 4.1 8.5 - - + -
112B PRO* 3.5 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU 4.1 17.3 - - - +
116A LEU* 2.6 16.1 + - + +
118A TRP* 1.3 96.6 - - + +
120A SER* 1.3 71.9 + - - +
122A VAL* 2.5 17.6 + - - +
123A ILE* 2.7 18.6 - - + +
109B ILE* 3.5 44.0 - - + +
112B PRO* 4.6 7.4 - - + -
113B PHE* 5.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 2.6 16.6 + - - +
117A THR 3.2 13.3 + - - -
119A ILE* 1.3 75.8 - - - +
121A GLY* 1.3 76.3 + - - -
123A ILE* 2.7 24.0 + - - +
124A LEU* 2.9 12.2 + - - +
198A PHE* 4.2 16.2 - - - -
201A LEU* 4.7 7.4 - - - -
202A HIS* 3.4 10.8 + - - -
205A MET* 3.3 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP 2.8 11.1 + - - -
120A SER* 1.3 83.6 + - - +
122A VAL* 1.3 65.2 + - - +
124A LEU* 2.6 25.3 + - - +
125A ALA 3.0 2.6 + - - -
202A HIS* 3.3 21.1 - - - -
302A HEM 3.1 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 2.7 30.5 + - + +
119A ILE* 2.5 22.3 + - + +
121A GLY* 1.3 65.7 - - - -
123A ILE* 1.3 61.1 + - + +
125A ALA* 2.4 36.9 + - + +
126A VAL* 3.3 11.2 + - + +
302A HEM 3.3 15.3 - - + +
105B PRO* 4.7 17.3 - - + +
108B LEU* 3.5 33.0 - - + -
109B ILE* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 2.7 45.3 - - + +
120A SER* 2.7 14.9 + - - +
122A VAL* 1.3 76.1 - - + +
124A LEU* 1.3 64.9 + - - +
126A VAL* 2.6 27.9 + - + +
127A ILE* 3.1 23.8 + - + +
198A PHE* 3.4 39.5 - - + -
109B ILE* 4.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER 2.9 5.4 + - - +
121A GLY* 2.6 22.6 + - - +
123A ILE* 1.3 72.3 - - - +
125A ALA* 1.3 49.7 + - - -
127A ILE* 3.7 6.7 + - - +
128A THR* 2.5 36.4 + - - -
195A ILE* 3.6 14.2 - - + +
198A PHE* 3.5 16.6 - - + +
199A MET* 3.5 39.5 - - + +
202A HIS* 3.1 45.1 - - + +
203A PHE* 6.1 0.2 - - + -
302A HEM 3.1 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 4.0 20.2 - - + -
121A GLY 3.0 2.8 + - - -
122A VAL* 2.4 22.0 + - + +
124A LEU* 1.3 70.6 - - - +
126A VAL* 1.3 59.0 + - + +
128A THR* 3.5 4.2 + - - -
129A VAL* 2.9 35.7 + - - +
302A HEM 3.7 19.7 - - + +
201B CLA 4.6 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.0 15.0 - - + +
123A ILE* 2.6 24.3 + - + +
125A ALA* 1.3 70.9 - - + +
127A ILE* 1.3 55.2 + - + +
129A VAL* 3.3 7.0 + - + +
130A SER* 2.3 49.2 + - - +
105B PRO* 4.9 14.8 - - + -
201B CLA 4.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.1 26.9 + - + +
124A LEU* 3.8 8.7 - - - +
126A VAL* 1.3 79.0 - - + +
128A THR* 1.3 68.8 + - - +
130A SER* 2.7 21.2 + - - -
131A PHE* 2.8 34.7 + - + -
191A LEU* 4.0 15.3 - - + -
194A LEU* 3.2 22.7 - - + -
195A ILE* 3.1 42.4 - - + +
198A PHE* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 3.7 27.8 - - + +
94A VAL* 4.5 19.3 - - + +
97A MET* 3.8 22.4 - - + -
124A LEU 2.5 22.3 + - - -
125A ALA 3.5 4.7 - - - -
127A ILE* 1.3 76.5 - - - +
129A VAL* 1.3 68.0 + - - +
131A PHE* 2.7 31.4 + - - +
132A GLY 3.7 1.6 + - - -
195A ILE* 4.5 4.7 - - - +
301A HEM 4.6 4.9 - - + +
302A HEM 3.1 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 5.2 10.3 - - + -
97A MET* 4.7 6.3 - - + -
125A ALA 2.9 27.4 + - - +
126A VAL* 3.6 4.7 - - + +
128A THR* 1.3 73.3 - - - +
130A SER* 1.3 62.9 + - - +
132A GLY* 3.1 11.8 + - - -
133A VAL* 3.7 10.5 + - + +
78B GLU* 5.2 1.0 - - - +
81B LEU* 3.6 44.2 - - + +
201B CLA 3.1 46.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 2.3 38.4 + - - +
127A ILE* 2.7 19.0 + - - -
129A VAL* 1.3 70.1 - - - +
131A PHE* 1.3 54.2 + - - -
132A GLY 3.3 0.5 + - - -
133A VAL* 3.6 11.7 + - - +
134A THR* 2.5 32.9 + - - +
191A LEU* 3.4 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.7 3.6 - + - -
127A ILE* 2.8 41.8 + - + -
128A THR* 2.7 22.4 + - - +
130A SER* 1.3 69.9 - - - +
132A GLY* 1.3 66.7 + - - +
134A THR* 2.8 6.7 + - - -
135A GLY 3.0 0.3 + - - -
187A HIS* 2.7 55.3 + + - -
191A LEU* 3.7 9.0 - - + -
192A PRO* 3.4 31.9 - - + -
195A ILE* 3.9 19.5 - - + -
301A HEM 3.4 58.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR 3.7 1.4 + - - -
129A VAL 3.1 8.3 + - - -
131A PHE* 1.3 79.4 - - - +
133A VAL* 1.3 51.1 + - - +
134A THR 2.3 17.7 + - - -
136A TYR* 2.5 30.0 + - - -
301A HEM 3.9 19.9 - - - +
78B GLU* 3.2 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.7 11.6 + - + +
130A SER* 3.7 12.8 - - - +
132A GLY* 1.3 69.2 - - - +
134A THR* 1.3 62.7 + - + +
136A TYR* 4.1 8.1 - - - -
137A SER* 4.0 1.4 + - - -
148A VAL* 3.1 30.3 - - + +
151A VAL* 4.0 30.7 - - + -
183A TYR* 3.9 11.8 - - + +
78B GLU* 3.8 6.8 + - + -
81B LEU* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER 2.5 20.1 + - - +
131A PHE* 2.8 10.0 + - - -
132A GLY 2.3 10.0 + - - -
133A VAL* 1.3 69.4 - - + +
135A GLY* 1.3 68.4 + - - +
137A SER* 2.8 23.7 + - - -
138A LEU* 3.4 9.3 + - - +
183A TYR* 3.5 51.6 - - + +
186A ALA* 4.1 11.2 - - + -
187A HIS* 3.7 13.0 + - - +
191A LEU* 4.5 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 2.8 4.4 + - - -
134A THR* 1.3 77.2 - - - +
136A TYR* 1.3 52.3 + - - +
137A SER 2.8 1.7 + - - -
138A LEU* 2.8 45.8 + - - +
139A PRO* 3.2 0.9 - - - +
187A HIS* 2.9 29.2 + - - -
301A HEM 3.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY* 2.5 31.7 + - - +
133A VAL* 3.8 4.0 - - - +
135A GLY* 1.3 68.9 - - - +
137A SER* 1.3 55.2 + - - +
139A PRO* 4.0 7.5 - - - +
143A VAL* 3.3 19.1 - - + +
144A GLY* 3.5 17.4 - - - -
147A ALA* 4.2 19.1 - - + -
148A VAL* 4.5 13.9 - - + -
301A HEM 3.4 23.8 - - + +
76B LEU 2.6 26.2 + - - -
78B GLU* 3.3 50.9 - - + +
79B TRP* 4.4 10.8 + + - -
----------------------------------------------------------
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