Contacts of the helix formed by residues 115 - 128 (chain A) in PDB entry 4WFH
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 ASP 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A SER 5.1 3.6 + - - +
112A SER* 2.8 34.7 + - - +
114A TRP* 1.3 82.3 - - - +
116A LEU* 1.3 66.5 + - - +
117A GLY* 3.7 3.7 + - - -
118A SER* 2.9 27.9 + - - -
119A ALA* 2.9 20.3 + - - +
249A ASP* 4.5 5.8 - - - +
51B ARG* 4.2 2.9 - - - +
55B GLN* 3.6 12.4 - - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 1.3 73.9 - - - +
117A GLY* 1.3 57.6 + - - +
119A ALA* 4.6 1.8 - - - -
120A PHE* 2.9 29.6 + - - +
44B VAL* 4.9 6.7 - - + +
47B ALA* 3.8 21.3 - - + +
48B LEU* 4.0 26.0 - - + +
51B ARG* 3.7 38.4 - - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.2 4.9 + - - -
116A LEU* 1.3 77.9 - - - +
118A SER* 1.3 57.2 + - - +
120A PHE* 3.4 7.1 - - - +
121A PHE* 3.1 25.6 + - - +
248A ALA 4.5 3.7 - - - +
250A PRO* 6.4 1.3 - - - -
258A GLN* 5.7 4.7 - - - -
262A TRP* 4.5 14.5 - - - -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER 3.3 4.3 + - - -
113A ALA* 3.2 28.7 - - - +
115A ASP* 2.9 20.6 + - - -
117A GLY* 1.3 75.0 - - - +
119A ALA* 1.3 59.2 + - - +
121A PHE* 3.4 5.5 + - - +
122A PHE* 2.8 28.6 + - - +
248A ALA* 3.2 12.9 + - - +
249A ASP* 2.7 28.4 + - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 4.1 1.2 + - - -
114A TRP* 4.2 25.8 - - + +
115A ASP 2.9 17.8 + - - +
116A LEU 3.9 2.2 - - - +
118A SER* 1.3 74.9 - - - +
120A PHE* 1.3 63.8 + - - +
122A PHE* 3.3 8.7 + - - +
123A SER* 2.9 28.6 + - - -
47B ALA* 3.5 29.2 - - + +
50B PHE* 4.4 3.2 - - + -
51B ARG* 4.4 2.9 - - + +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 2.9 19.6 + - - +
117A GLY* 3.4 8.1 - - - +
119A ALA* 1.3 75.2 - - - +
121A PHE* 1.3 66.6 + - - +
123A SER* 3.0 8.3 + - - -
124A GLY* 3.0 18.7 + - - -
262A TRP* 3.8 44.6 - + + -
40B LEU* 4.1 17.0 - - + -
43B LEU* 3.2 49.4 - - + +
44B VAL* 3.9 29.2 - - + -
47B ALA* 3.4 9.7 - - + +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY 3.1 11.7 + - - +
118A SER* 3.4 11.7 - - - +
119A ALA 3.3 0.2 - - - -
120A PHE* 1.3 85.2 - - - +
122A PHE* 1.3 64.3 + - + +
124A GLY* 3.0 5.4 + - - +
125A THR* 3.0 37.9 + - + +
132A TYR* 3.9 24.0 - + - -
134A ASN* 5.3 4.5 - - - -
245A VAL* 4.0 17.0 - - + -
247A GLY* 3.7 20.2 - - - +
248A ALA* 3.8 29.4 - - + +
261A VAL* 5.6 0.4 - - + -
262A TRP* 3.5 31.6 - + - +
265A ILE* 4.9 13.5 - - + -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 5.6 0.9 - - - +
114A TRP* 3.6 28.5 - + + -
118A SER 2.8 20.2 + - - +
119A ALA* 3.6 7.9 - - - +
120A PHE 3.3 0.2 - - - -
121A PHE* 1.3 76.2 - - - +
123A SER* 1.3 63.3 + - - +
125A THR* 2.4 35.1 + - + -
126A ILE* 3.4 13.5 + - + +
133A GLY* 5.7 2.0 - - - -
135A VAL* 3.8 24.9 - - + -
137A LEU* 3.8 21.1 - - + -
50B PHE* 3.7 36.6 - + - -
241B PHE* 3.6 37.5 - + - -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 2.9 14.1 + - - -
120A PHE 3.0 8.9 + - - -
122A PHE* 1.3 75.9 - - - +
124A GLY* 1.3 63.2 + - - +
126A ILE* 3.0 22.0 + - - +
127A ILE* 3.3 16.6 + - - +
149A TYR* 3.5 25.5 - - - -
43B LEU* 3.9 12.1 - - - -
46B GLY 3.6 0.9 - - - -
47B ALA 3.6 10.0 + - - -
50B PHE* 3.3 20.6 - - - -
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE 3.0 12.3 + - - -
121A PHE* 3.0 5.6 + - - -
123A SER* 1.3 76.9 - - - +
125A THR* 1.3 51.5 + - - +
126A ILE 3.1 1.4 + - - -
127A ILE* 3.6 4.2 - - - +
128A THR* 2.6 42.9 + - - +
43B LEU* 3.6 16.2 - - - +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 3.0 41.1 + - + +
122A PHE* 2.4 37.0 + - + -
124A GLY* 1.3 75.0 - - - +
126A ILE* 1.3 59.4 + - - +
128A THR* 3.4 6.7 - - - -
129A THR 3.7 0.7 - - - -
130A ILE* 3.1 13.1 + - + -
131A GLY* 2.8 39.2 + - - +
132A TYR* 3.9 21.3 - - + +
133A GLY 5.6 0.7 + - - +
239B VAL* 4.3 0.3 - - - +
241B PHE* 4.3 6.4 - - - -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.4 25.4 - - + +
123A SER* 3.3 6.1 - - - +
124A GLY 3.0 0.6 - - - -
125A THR* 1.3 75.3 - - - +
127A ILE* 1.3 58.7 + - - +
128A THR 3.2 1.6 - - - -
129A THR* 2.7 25.8 + - - -
146A CYS* 3.7 18.2 - - - -
149A TYR* 4.1 11.7 - - + -
150A ALA* 3.5 35.2 - - + -
154A ILE* 3.8 8.1 - - - +
50B PHE* 3.6 33.4 - - + -
239B VAL* 4.1 13.3 - - + +
241B PHE* 4.0 15.7 - - + -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER 3.3 3.6 + - - +
124A GLY* 3.6 10.1 - - - +
126A ILE* 1.3 77.7 - - + +
128A THR* 1.3 63.9 + - + +
129A THR* 3.1 3.3 + - - +
149A TYR* 3.9 26.7 - - + +
153A GLY* 3.7 35.0 - - - +
154A ILE* 3.7 24.8 - - - +
156A LEU* 6.6 0.4 - - + -
157A PHE* 3.7 41.8 - - + -
39B VAL* 4.4 9.4 - - + -
42B TYR* 4.2 6.5 - - + -
43B LEU* 3.5 30.7 - - + -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY* 2.6 26.3 + - - +
125A THR* 3.3 7.8 + - - -
127A ILE* 1.3 76.8 - - + +
129A THR* 1.3 72.1 + - - +
130A ILE* 3.1 32.2 + - + +
157A PHE* 3.8 34.8 - - + -
238A THR* 4.0 12.6 - - - +
265A ILE* 4.8 5.2 - - + -
269A LEU* 4.0 15.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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