Contacts of the helix formed by residues 112 - 130 (chain A) in PDB entry 2FW0
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A THR 3.4 3.0 + - - -
111A ASP* 1.3 72.1 - - - +
113A LYS* 1.3 62.5 + - - +
115A SER* 2.7 32.7 + - - -
116A GLY 3.8 0.7 + - - -
153A PRO* 4.9 3.6 - - - -
154A ASP* 2.6 40.5 + - - +
157A ALA* 4.2 12.5 - - - +
158A ARG* 4.5 1.7 + - - +
295A TYR* 3.7 15.2 + - - -
311A NA 4.4 0.4 - - - -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 3.9 28.4 + - + +
112A SER* 1.3 77.8 - - - +
114A GLU* 1.3 68.6 + - + +
116A GLY* 3.0 5.5 + - - +
117A ILE* 3.0 31.5 + - + +
157A ALA* 3.8 16.1 - - + +
161A TYR* 3.6 53.7 + - + +
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Residues in contact with GLU 114 (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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110A THR* 3.2 24.1 - - - +
111A ASP* 3.0 31.7 + - + +
113A LYS* 1.3 84.1 - - + +
115A SER* 1.3 56.3 + - - +
117A ILE* 3.6 15.2 - - + +
118A ILE* 2.8 37.9 + - + +
292A ARG* 5.3 10.2 - - - +
294A PRO* 4.8 8.0 - - - +
295A TYR* 3.7 12.3 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 2.7 23.3 + - - -
114A GLU* 1.3 78.7 - - - +
116A GLY* 1.3 57.5 + - - +
118A ILE* 4.0 1.2 - - - +
119A GLN* 3.0 28.2 + - - +
158A ARG* 2.9 33.5 + - - +
235A VAL* 4.5 10.7 - - - +
254A VAL* 4.2 6.0 - - - +
295A TYR* 3.5 39.6 - - - -
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Residues in contact with GLY 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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112A SER 3.8 0.4 + - - -
113A LYS 3.0 7.4 + - - -
115A SER* 1.3 80.4 + - - +
117A ILE* 1.3 58.3 + - - +
119A GLN* 3.3 6.4 + - - +
120A GLY 2.9 23.7 + - - -
158A ARG* 4.1 20.9 - - - +
161A TYR* 4.3 1.6 - - - -
162A VAL* 3.3 28.9 - - - -
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Residues in contact with ILE 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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113A LYS* 3.0 26.5 + - + +
114A GLU* 3.3 18.8 + - + +
116A GLY* 1.3 76.8 - - - +
118A ILE* 1.3 63.1 + - + +
120A GLY 3.1 1.4 + - - -
121A ASP* 2.9 34.5 + - - +
161A TYR* 4.1 24.7 - - + -
165A GLU* 3.4 40.1 - - + +
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Residues in contact with ILE 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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114A GLU* 2.8 27.4 + - + +
115A SER 4.1 3.1 - - - +
117A ILE* 1.3 72.6 - - + +
119A GLN* 1.4 66.7 + - - +
121A ASP* 3.3 17.1 + - + +
122A LEU* 2.9 22.0 + - - +
254A VAL* 3.8 11.4 - - + -
294A PRO* 6.1 1.6 - - + -
295A TYR* 3.7 26.7 - - + +
296A VAL 3.8 6.1 - - - -
297A GLY* 3.4 31.0 - - - +
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Residues in contact with GLN 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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115A SER 3.0 18.5 + - - +
116A GLY* 3.7 5.9 - - - +
117A ILE 3.3 0.4 - - - -
118A ILE* 1.4 76.9 - - - +
120A GLY* 1.3 58.2 + - - +
122A LEU* 3.2 6.5 + - + +
123A ILE* 2.9 39.3 + - + +
158A ARG* 4.7 5.4 - - - +
162A VAL* 3.4 21.8 - - + +
208A ILE* 3.5 17.3 - - - +
209A ALA 3.0 25.9 + - - +
210A ASN* 5.4 1.4 + - - -
233A PHE* 3.6 17.0 + - + +
234A GLY 3.0 25.7 + - - +
235A VAL* 3.6 8.8 - - + +
254A VAL* 3.7 13.6 - - + +
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Residues in contact with GLY 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 GLY 2.9 12.9 + - - -
117A ILE 3.6 3.1 - - - -
119A GLN* 1.3 75.4 - - - +
121A ASP* 1.4 59.5 + - - +
123A ILE* 3.3 1.6 + - - -
124A ALA* 2.9 25.6 + - - +
162A VAL* 3.7 28.9 - - - +
165A GLU* 4.3 6.7 - - - -
166A LEU* 3.4 15.5 - - - +
169A LYS* 5.4 0.4 - - - -
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Residues in contact with ASP 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 ILE* 2.9 24.7 + - - +
118A ILE* 3.7 17.5 - - + +
120A GLY* 1.4 78.1 - - - +
122A LEU* 1.3 56.2 + - - +
124A ALA* 3.3 7.0 + - - +
125A LYS* 2.9 28.8 + - - +
165A GLU* 2.4 34.9 - - - +
169A LYS* 3.2 22.2 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE 2.9 13.6 + - - +
119A GLN* 3.2 10.7 + - + +
121A ASP* 1.3 74.1 - - - +
123A ILE* 1.3 67.1 + - - +
125A LYS* 3.3 11.9 + - + +
126A HIS* 3.1 41.0 + - + +
233A PHE* 4.1 9.0 - - + -
252A GLY* 3.8 10.5 - - - -
253A THR* 3.2 42.0 - - - +
254A VAL* 4.6 4.5 - - + -
297A GLY* 4.3 16.4 - - - -
298A VAL 3.9 2.2 - - - +
299A ASP* 3.4 30.3 - - + +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 2.9 27.2 + - + +
120A GLY 3.7 4.3 - - - +
122A LEU* 1.3 76.7 - - - +
124A ALA* 1.3 56.4 + - - +
126A HIS* 3.2 2.3 + - - +
127A TRP* 2.8 33.0 + - + +
133A TRP* 5.0 0.6 - - + -
141A ILE* 4.0 17.0 - - + -
162A VAL* 3.7 25.4 - - + -
166A LEU* 3.9 16.8 - - + -
206A VAL* 4.4 15.3 - - + -
208A ILE* 3.8 24.7 - - + -
233A PHE* 3.6 38.7 - - + -
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Residues in contact with ALA 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 GLY 2.9 17.1 + - - +
121A ASP 3.6 5.2 - - - +
122A LEU 3.3 0.2 - - - -
123A ILE* 1.3 76.5 - - - +
125A LYS* 1.3 62.9 + - - +
127A TRP* 3.9 1.2 - - - +
128A ALA* 3.0 27.7 + - - +
166A LEU* 3.8 3.6 - - + +
169A LYS* 3.9 24.0 - - + -
171A ILE* 3.6 31.4 - - + +
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Residues in contact with LYS 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 ASP 2.9 14.7 + - - +
122A LEU* 3.4 16.0 - - + +
123A ILE 3.2 0.2 - - - -
124A ALA* 1.3 77.5 - - - +
126A HIS* 1.3 71.5 + - + +
128A ALA* 4.1 3.7 - - - +
129A ALA* 3.4 21.5 + - + +
299A ASP* 2.7 32.2 + - - +
301A ASP* 2.7 32.2 + - - +
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Residues in contact with HIS 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 LEU* 3.1 35.7 + - + +
123A ILE 4.0 1.6 - - - +
125A LYS* 1.3 85.0 - - + +
127A TRP* 1.3 67.1 + - - +
129A ALA* 3.2 3.3 + - - +
130A ASN* 2.9 38.3 + - - +
133A TRP* 3.5 26.1 - + + -
233A PHE* 4.0 12.8 - + + -
251A ALA* 4.3 9.1 + - - +
299A ASP* 2.7 43.7 + - + +
300A LYS* 5.3 1.8 - - + -
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Residues in contact with TRP 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 ILE* 2.8 24.1 + - + +
124A ALA* 3.9 4.0 - - - +
126A HIS* 1.3 71.2 - - - +
128A ALA* 1.3 67.8 + - + +
130A ASN 3.1 21.6 + - - +
131A GLN* 4.0 2.6 + - - +
133A TRP* 3.8 46.6 - + + -
134A ASP* 3.5 28.7 - - + -
139A GLY* 4.2 8.8 + - - -
140A GLN 3.4 30.7 - - - -
141A ILE* 3.5 36.1 - - + -
171A ILE* 3.8 30.6 - - + +
205A GLU* 3.4 15.3 - - + -
206A VAL* 4.4 4.0 - - + -
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Residues in contact with ALA 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 ALA 3.0 19.2 + - - +
125A LYS* 4.1 4.3 - - - +
127A TRP* 1.3 83.3 - - + +
129A ALA* 1.3 59.3 + - - +
130A ASN 3.6 0.3 + - - -
131A GLN* 4.7 14.6 + - - +
171A ILE* 6.0 1.6 - - + -
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Residues in contact with ALA 129 (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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125A LYS 3.4 15.1 + - - +
126A HIS* 3.2 7.4 + - - +
128A ALA* 1.3 80.1 - - - +
130A ASN* 1.4 67.4 + - - +
131A GLN 3.9 2.0 + - - -
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Residues in contact with ASN 130 (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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126A HIS* 2.9 34.8 + - - +
127A TRP* 3.1 11.0 + - - +
128A ALA 3.3 0.2 - - - -
129A ALA* 1.4 89.0 - - - +
131A GLN* 1.3 60.1 + - - +
132A GLY 3.1 3.4 - - - +
133A TRP* 2.9 62.0 + - + +
134A ASP 4.5 0.5 + - - -
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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