Contacts of the strand formed by residues 124 - 135 (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 LYS 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLY* 3.1 4.9 - - - -
135A VAL* 2.8 47.0 + - + +
140A SER* 3.0 30.1 + - - +
144A ASN 3.8 16.0 + - - -
37B HIS* 6.2 2.5 - - - +
118B ALA* 5.4 0.2 - - - -
122B GLY 3.8 2.4 + - - +
123B PHE* 1.3 72.7 - - - +
125B VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 125 (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* 3.5 29.4 - - + -
133A TYR 3.9 2.7 - - - -
134A GLY* 4.4 0.7 - - - -
85B ASP* 5.4 4.2 - - - +
114B GLU* 3.5 57.9 - - + +
117B ALA* 5.1 1.6 - - + -
118B ALA* 4.1 18.3 - - + +
123B PHE* 3.8 8.5 + - + +
124B LYS* 1.3 73.9 - - - +
126B SER* 1.3 63.1 + - - +
127B HIS 4.0 4.3 - - - +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 3.7 14.6 + - - -
133A TYR 2.8 14.8 + - - -
134A GLY* 4.2 3.4 - - - -
73B LYS* 5.9 1.0 + - - -
85B ASP* 6.0 2.0 - - - -
86B PHE 5.4 2.9 + - - -
88B THR* 4.0 17.8 + - - +
90B ASP* 4.8 0.5 - - - +
114B GLU* 4.8 2.3 - - - +
124B LYS 3.8 1.6 + - - -
125B VAL* 1.3 75.9 - - - +
127B HIS* 1.3 80.6 + - - +
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Residues in contact with HIS 127 (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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97A GLU* 3.4 29.6 + - - -
132A ILE* 3.7 3.0 - - - +
133A TYR* 2.7 57.2 + + + +
88B THR* 3.4 43.4 - - + +
89B SER 3.8 9.4 - - - +
90B ASP* 3.3 15.9 - - - +
91B HIS* 5.9 2.2 - + - -
114B GLU* 4.2 6.3 - - - -
125B VAL* 4.0 1.0 - - - +
126B SER* 1.3 101.2 + - - +
128B HIS* 1.3 67.7 + - - +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.1 11.2 - - + -
131A GLU 3.2 13.9 - - - +
132A ILE* 4.2 9.2 - - + -
133A TYR* 4.4 4.9 - - - -
89B SER 4.5 1.2 - - - +
90B ASP* 2.9 37.3 + - + -
91B HIS* 3.0 25.4 + - - -
92B TYR* 2.8 36.0 + + - -
109B GLY* 4.4 1.1 - - - -
110B LEU* 3.6 41.2 - - + +
114B GLU* 2.7 29.7 + - + +
127B HIS* 1.3 78.6 - - - +
129B ARG* 1.3 60.9 + - - +
130B LEU 4.7 0.4 - - - -
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Residues in contact with ARG 129 (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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129A ARG* 2.7 35.8 - - - +
130A LEU* 3.7 3.2 - - - -
131A GLU* 2.7 56.4 + - - +
133A TYR* 3.8 22.0 + - + -
91B HIS* 3.4 13.2 - - + +
93B HIS* 4.1 24.0 + - + +
128B HIS* 1.3 74.5 - - - +
130B LEU* 1.3 61.6 + - - +
131B GLU* 3.6 26.7 + - + -
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Residues in contact with LEU 130 (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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110A LEU* 3.8 30.3 - - + -
113A VAL* 3.7 29.8 - - + -
128A HIS* 4.0 15.9 - - + -
129A ARG 3.6 13.5 - - - +
130A LEU* 4.0 17.0 - - + -
91B HIS 2.9 7.1 + - - +
92B TYR* 3.5 25.5 - - + -
93B HIS* 3.0 27.9 + - - +
105B PHE* 4.7 1.6 - - + -
110B LEU* 4.6 7.9 - - + -
128B HIS* 4.2 0.8 - - + -
129B ARG* 1.3 73.9 - - - +
131B GLU* 1.3 63.0 + - - +
132B ILE* 4.0 16.8 - - + -
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Residues in contact with GLU 131 (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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128A HIS* 3.1 5.9 - - - +
129A ARG* 2.6 74.6 + - - +
93B HIS* 3.5 12.6 - - + -
95B ILE* 3.8 20.5 - - + +
129B ARG* 3.6 27.4 + - + -
130B LEU* 1.3 75.7 - - - +
132B ILE* 1.3 61.5 + - - +
133B TYR* 2.6 38.5 + - + -
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Residues in contact with ILE 132 (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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113A VAL* 4.3 3.8 - - + -
114A GLU* 4.2 19.5 - - + -
117A ALA* 3.7 15.9 - - + -
123A PHE* 5.1 1.9 - - + -
125A VAL* 3.4 39.7 - - + -
127A HIS 3.7 4.9 - - - +
128A HIS* 4.2 6.1 - - + -
93B HIS 2.8 16.2 + - - +
94B ALA* 3.3 9.0 - - + +
95B ILE* 2.7 31.9 + - - +
105B PHE* 3.7 24.2 - - + -
130B LEU* 4.0 23.1 - - + -
131B GLU* 1.3 75.9 - - - +
133B TYR* 1.3 61.0 + - - +
134B GLY 4.0 0.2 + - - -
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Residues in contact with TYR 133 (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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123A PHE* 5.3 0.2 - - - -
125A VAL* 3.8 3.3 - - - +
126A SER* 2.8 23.9 + - - -
127A HIS* 2.8 58.1 + + + +
128A HIS* 4.3 1.3 - - - -
129A ARG* 4.1 24.1 + - + -
95B ILE* 3.4 38.3 - - + +
97B GLU* 4.0 15.3 - - + -
131B GLU* 2.6 45.0 + - + -
132B ILE* 1.3 75.8 - - - +
134B GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 134 (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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123A PHE* 4.1 7.2 - - - -
124A LYS 3.1 14.6 - - - -
125A VAL* 4.3 0.4 - - - -
126A SER* 3.9 9.9 - - - -
95B ILE 3.0 8.9 + - - -
96B CYS* 3.3 1.4 - - - -
97B GLU* 2.8 38.6 + - - +
132B ILE 4.0 0.6 + - - -
133B TYR* 1.3 76.8 - - - +
135B VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 135 (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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35A MET* 6.0 0.9 - - + -
122A GLY 4.5 0.2 - - - +
123A PHE* 3.3 3.9 - - - -
124A LYS* 2.9 41.6 + - + +
96B CYS* 3.8 5.6 - - - -
97B GLU* 5.3 6.5 - - + +
98B ASN* 4.7 3.1 - - + -
134B GLY* 1.3 79.9 - - - +
136B CYS* 1.3 70.9 + - - +
139B CYS* 3.5 19.3 - - + -
140B SER* 3.8 10.4 - - - +
143B GLU* 3.4 34.5 - - - +
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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