Contacts of the helix formed by residues 122 - 139 (chain A) in PDB entry 2FX0
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 PHE 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.8 13.7 - + + -
65A ALA* 4.8 3.8 - - - -
107A GLU* 4.9 3.4 - - + -
108A ILE* 3.5 51.8 - - + -
115A LEU* 4.0 15.5 - - + -
118A ILE* 3.6 24.0 - - + -
119A LYS* 2.7 47.0 + - + -
121A TYR* 1.3 81.8 - - - +
123A ILE* 1.3 66.5 + - + +
124A GLY 3.2 3.8 - - - -
125A SER* 3.3 14.2 + - - -
126A PHE* 3.2 27.2 - + + -
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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
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119A LYS* 2.8 53.4 + - + +
120A PRO* 4.4 8.7 - - + +
121A TYR 4.3 0.2 - - - +
122A PHE* 1.3 78.1 - - + +
124A GLY* 1.3 59.4 + - - +
126A PHE* 3.3 8.4 + - + +
127A GLU* 2.9 45.7 + - + +
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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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65A ALA* 4.7 11.2 - - - +
68A LEU* 5.8 0.4 - - - -
120A PRO 5.7 1.0 + - - -
122A PHE 3.2 1.0 - - - -
123A ILE* 1.3 80.6 - - - +
125A SER* 1.3 58.8 + - - +
126A PHE 3.1 0.2 - - - -
127A GLU* 3.8 7.6 - - - +
128A GLN* 2.9 35.5 + - - +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 5.1 0.9 - - - +
65A ALA* 4.0 16.4 + - - +
68A LEU* 3.8 16.3 - - - +
86A TYR* 2.7 25.9 + - - -
90A PHE* 3.1 33.4 - - - -
122A PHE* 3.3 16.5 + - - -
124A GLY* 1.3 75.9 - - - +
126A PHE* 1.3 63.2 - - - +
128A GLN* 4.7 2.2 - - - -
129A LEU 3.3 12.6 + - - -
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Residues in contact with PHE 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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86A TYR* 4.8 0.9 - - - -
108A ILE* 3.8 39.3 - - + -
109A ILE* 6.3 0.7 - - + -
122A PHE* 3.2 30.5 - + + -
123A ILE* 3.3 11.6 + - + +
124A GLY 3.1 0.4 - - - -
125A SER* 1.3 82.7 - - - +
127A GLU* 1.3 66.2 + - - +
128A GLN 3.2 1.8 - - - -
129A LEU* 3.5 9.2 + - + +
130A LYS* 3.1 23.6 + - - +
151A ILE* 4.3 22.9 - - + +
155A THR* 3.6 36.6 - - + -
159A LEU* 5.3 3.1 - - + -
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Residues in contact with GLU 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* 2.9 40.8 + - - +
124A GLY* 3.3 8.5 + - - +
126A PHE* 1.3 76.7 - - - +
128A GLN* 1.3 57.1 + - - +
130A LYS* 3.4 21.4 + - - +
131A GLU* 3.0 39.4 + - + +
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Residues in contact with GLN 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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68A LEU* 4.3 17.2 + - - +
69A PRO 3.3 13.2 + - - +
70A ASN* 3.3 17.1 + - - +
71A PHE* 2.8 43.8 + - - +
72A LEU 4.4 1.0 + - - -
86A TYR* 4.2 7.9 - - + -
124A GLY 2.9 18.1 + - - +
125A SER 4.1 4.3 - - - +
127A GLU* 1.3 73.1 - - - +
129A LEU* 1.3 65.9 + - - +
130A LYS 3.1 0.9 - - - -
131A GLU* 2.9 18.3 + - - +
132A ILE* 2.9 39.1 + - + +
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Residues in contact with LEU 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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83A LEU* 3.8 27.8 - - + -
86A TYR* 3.4 36.0 - - + +
87A LEU* 5.0 0.2 - - + -
125A SER 3.3 8.1 + - - +
126A PHE* 3.8 9.4 - - + +
128A GLN* 1.3 77.1 - - - +
130A LYS* 1.3 57.4 + - - +
132A ILE* 3.3 5.8 + - - +
133A LEU* 2.9 50.6 + - + +
151A ILE* 4.2 28.3 - - + -
154A ILE* 4.5 22.7 - - + -
155A THR* 4.6 7.2 - - - +
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Residues in contact with LYS 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 PHE 3.1 14.5 + - - +
127A GLU* 3.4 26.4 + - - +
128A GLN 3.1 0.2 - - - -
129A LEU* 1.3 76.4 - - - +
131A GLU* 1.3 56.9 + - - +
133A LEU* 3.9 0.9 - - - +
134A GLN* 2.9 68.7 + - + +
147A ILE* 4.3 16.8 - - + +
148A ASN* 4.7 10.7 + - - -
151A ILE* 4.0 23.9 - - + +
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Residues in contact with GLU 131 (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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70A ASN* 3.8 21.6 + - - -
72A LEU* 3.9 18.3 - - + +
127A GLU* 3.0 28.3 + - + +
128A GLN* 2.9 18.8 + - - +
130A LYS* 1.3 75.8 - - - +
132A ILE* 1.3 58.3 + - + +
134A GLN* 3.4 7.3 + - - +
135A GLU* 2.8 32.9 + - - +
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Residues in contact with ILE 132 (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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71A PHE* 4.1 14.8 - - + -
72A LEU* 4.0 23.1 - - + +
79A PRO* 3.5 27.2 - - + +
82A ALA* 4.1 12.8 - - + +
83A LEU* 3.6 22.4 - - + +
86A TYR* 3.9 36.6 - - + -
128A GLN* 2.9 26.2 + - + +
129A LEU* 3.8 4.9 - - - +
131A GLU* 1.3 76.7 - - - +
133A LEU* 1.3 63.7 + - - +
135A GLU* 3.3 1.4 + - - +
136A GLY* 3.0 21.0 + - - -
142A PHE* 4.0 3.5 - - + -
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Residues in contact with LEU 133 (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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83A LEU* 4.4 10.1 - - + -
129A LEU* 2.9 42.5 + - + +
130A LYS 4.0 0.2 - - - +
132A ILE* 1.3 76.4 - - - +
134A GLN* 1.3 57.3 + - - +
136A GLY* 3.4 2.1 + - - -
137A GLU* 2.9 27.9 + - - +
142A PHE* 3.6 11.4 - - + -
144A PHE* 3.8 9.9 - - + -
147A ILE* 3.7 27.8 - - + -
150A THR* 4.1 13.0 - - + -
151A ILE* 3.9 12.3 - - + -
154A ILE* 3.9 12.1 - - + -
195A LEU* 3.5 38.1 - - + -
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Residues in contact with GLN 134 (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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130A LYS* 2.9 57.2 + - - +
131A GLU* 4.0 5.3 - - - +
133A LEU* 1.3 74.2 - - - +
135A GLU* 1.3 58.5 + - - +
137A GLU* 3.3 15.4 + - - +
138A LYS* 2.8 30.7 + - - +
147A ILE* 4.0 23.2 - - + +
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Residues in contact with GLU 135 (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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72A LEU* 3.9 31.1 - - + +
77A PHE* 4.2 14.7 - - - +
79A PRO* 4.2 3.1 - - + -
131A GLU 2.8 21.8 + - - +
132A ILE 3.8 3.4 - - - +
134A GLN* 1.3 71.7 - - - +
136A GLY* 1.3 57.6 + - - +
138A LYS* 2.8 41.4 + - - +
139A GLN* 2.8 67.1 + - - +
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Residues in contact with GLY 136 (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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79A PRO* 3.5 19.6 - - - +
132A ILE 3.0 10.3 + - - -
133A LEU 3.7 0.2 - - - -
135A GLU* 1.3 74.0 - - - +
137A GLU* 1.3 62.4 + - - +
139A GLN 3.4 1.0 + - - -
140A GLY 3.1 3.6 + - - -
141A VAL* 3.0 29.9 + - - +
142A PHE* 3.2 26.9 + - - -
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Residues in contact with GLU 137 (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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133A LEU 2.9 16.4 + - - +
134A GLN* 3.3 13.6 + - - +
136A GLY* 1.3 71.5 - - - +
138A LYS* 1.3 62.2 + - - +
140A GLY* 2.9 20.6 + - - -
142A PHE* 3.6 19.6 - - - +
143A HIS* 5.5 0.9 - - - -
144A PHE* 3.3 46.1 + - + +
147A ILE* 5.4 0.9 - - - +
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Residues in contact with LYS 138 (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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134A GLN 2.8 19.8 + - - +
135A GLU* 2.8 45.4 + - - +
137A GLU* 1.3 73.7 - - - +
139A GLN* 1.3 57.9 + - + +
140A GLY* 3.2 4.3 + - - -
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Residues in contact with GLN 139 (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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77A PHE* 2.8 26.3 + - - +
78A ASN* 5.1 0.2 - - - -
79A PRO* 3.4 23.4 - - + +
135A GLU* 2.8 46.7 + - - +
136A GLY 3.9 4.7 - - - +
137A GLU 3.2 0.2 - - - -
138A LYS* 1.3 76.9 - - + +
140A GLY* 1.3 57.9 + - - +
141A VAL* 3.3 10.1 + - + +
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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