Contacts of the helix formed by residues 110 - 122 (chain B) in PDB entry 2FE3
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 LEU 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.8 12.3 - - + -
113A VAL* 3.7 29.8 - - + -
130A LEU* 3.7 27.4 - - + -
92B TYR* 4.3 9.2 - - + -
107B TYR* 4.0 7.0 - - + -
109B GLY* 1.3 79.9 - - - +
111B ASP* 1.3 66.1 + - - +
112B GLU 3.3 2.5 - - - -
113B VAL* 3.1 14.4 + - + -
114B GLU* 2.9 25.5 + - + +
128B HIS* 3.6 41.0 - - + +
130B LEU* 4.6 8.3 - - + -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO 5.7 0.3 - - - +
109B GLY 3.7 3.0 - - - +
110B LEU* 1.3 76.7 - - - +
112B GLU* 1.3 64.7 + - - +
114B GLU* 3.4 8.7 + - - +
115B GLN* 2.9 54.4 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.1 25.2 + - + +
110B LEU 3.3 0.6 - - - -
111B ASP* 1.3 86.3 + - - +
113B VAL* 1.3 64.1 - - + +
115B GLN* 3.5 9.9 + - - +
116B LEU* 3.0 24.6 + - + +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 5.3 0.2 - - + -
105A PHE* 4.4 8.6 - - + -
107A TYR* 3.6 41.5 - - + +
110A LEU* 3.6 22.9 - - + -
130A LEU* 3.5 29.2 - - + -
132A ILE* 4.2 7.0 - - + -
110B LEU* 3.1 22.3 + - + +
112B GLU* 1.3 74.9 - - + +
114B GLU* 1.3 55.7 + - - +
116B LEU* 3.3 1.9 + - - +
117B ALA* 2.8 33.4 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.3 16.6 - - + -
90B ASP* 4.2 1.2 - - - +
110B LEU* 2.9 22.1 + - + +
111B ASP* 3.8 7.3 - - - +
113B VAL* 1.3 76.0 - - - +
115B GLN* 1.3 60.2 + - + +
117B ALA* 3.7 1.2 - - - +
118B ALA* 3.0 30.5 + - - +
125B VAL* 3.5 36.0 - - + +
126B SER 4.8 1.6 - - - +
127B HIS* 4.2 9.2 - - - -
128B HIS* 2.7 36.0 + - - +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP* 2.9 42.9 + - - +
112B GLU* 3.9 7.2 - - - +
114B GLU* 1.3 77.7 - - + +
116B LEU* 1.3 63.7 + - - +
118B ALA* 3.5 6.2 + - - +
119B HIS* 3.2 20.6 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 6.2 0.9 - - + -
106A HIS 4.7 9.9 - - - +
107A TYR* 3.6 31.2 - - + -
108A PRO* 5.2 4.5 - - + -
112B GLU* 3.0 18.1 + - + +
113B VAL 3.8 2.7 - - - +
115B GLN* 1.3 77.8 - - - +
117B ALA* 1.3 63.2 + - - +
119B HIS* 3.0 16.0 + - + +
120B VAL* 2.9 40.3 + - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 5.8 2.0 - - + -
105A PHE* 3.6 22.5 - - + -
132A ILE* 3.6 29.2 - - + -
113B VAL 2.8 21.6 + - - +
114B GLU 3.7 3.1 - - - +
116B LEU* 1.3 71.7 - - - +
118B ALA* 1.3 57.7 + - - +
120B VAL* 3.9 9.2 - - - -
121B THR* 2.7 38.9 + - + +
125B VAL* 5.1 1.8 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU 3.0 17.4 + - - +
115B GLN* 3.8 7.0 - - - +
117B ALA* 1.3 76.2 - - - +
119B HIS* 1.3 58.4 + - - +
121B THR* 4.1 2.9 - - - -
122B GLY* 2.9 31.0 + - - -
123B PHE 3.2 23.1 - - - +
124B LYS* 5.4 0.2 - - - -
125B VAL* 4.1 12.5 - - + +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLN 3.2 12.6 + - - +
116B LEU* 3.0 18.9 + - + +
118B ALA* 1.3 79.5 - - - +
120B VAL* 1.3 75.5 + - + +
122B GLY* 4.0 4.2 + - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.8 31.4 - - + -
106A HIS 5.3 3.6 - - - +
116B LEU* 2.9 36.7 + - + +
117B ALA* 3.7 9.4 - - - +
119B HIS* 1.3 92.1 - - + +
121B THR* 1.3 63.7 + - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 4.1 7.7 - - + +
103A VAL* 4.0 25.0 - - + +
105A PHE* 4.0 27.6 - - + -
137A GLN* 4.9 7.0 + - - +
117B ALA* 2.7 25.4 + - - +
120B VAL* 1.3 90.7 - - + +
122B GLY* 1.3 57.0 + - - +
123B PHE* 3.1 40.7 + - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A CYS 4.4 0.2 - - - -
137A GLN* 3.8 42.6 + - - +
140A SER* 5.7 1.2 - - - -
118B ALA 2.9 14.0 + - - -
119B HIS 4.0 3.2 + - - -
120B VAL 3.6 1.8 - - - -
121B THR* 1.3 77.0 - - - +
123B PHE* 1.3 64.6 + - - +
124B LYS* 3.8 2.3 + - - +
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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