Contacts of the helix formed by residues 125 - 137 (chain B) in PDB entry 4H3E
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 PRO 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ALA 3.3 8.3 - - - +
124B MET* 1.3 85.4 - - + +
126B LYS* 1.3 65.8 - - - +
127B SER* 3.2 7.0 - - - +
128B PHE* 3.2 6.9 + - + +
129B GLU* 3.0 20.0 + - - +
221B TRP* 3.6 19.5 - - + +
222B GLU* 4.4 13.5 - - + -
225B ALA* 3.6 24.5 - - + -
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Residues in contact with LYS 126 (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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124B MET 3.6 1.4 + - - -
125B PRO* 1.3 73.6 - - - +
127B SER* 1.3 63.9 + - - +
129B GLU* 3.4 10.8 + - - +
130B SER* 3.0 25.5 + - - -
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Residues in contact with SER 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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125B PRO* 3.2 4.8 - - - +
126B LYS* 1.3 81.1 - - - +
128B PHE* 1.3 61.4 + - - +
130B SER* 3.5 6.3 + - - -
131B ALA* 3.3 19.8 + - - +
228B HIS* 5.4 3.7 + - - -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 4.1 17.0 - - + -
125B PRO* 3.2 8.8 + - + +
127B SER* 1.3 77.6 - - - +
129B GLU* 1.3 66.1 + - - +
131B ALA* 3.1 6.2 + - + +
132B VAL* 3.1 44.1 + - + +
161B LEU* 3.9 15.9 - - + -
171B LEU* 4.6 6.3 - - + -
190B VAL* 4.4 5.6 - - + -
221B TRP* 3.8 28.7 - + - -
224B VAL* 3.6 21.5 - - + -
225B ALA* 3.7 27.8 - - + +
228B HIS* 3.7 42.8 - + + +
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Residues in contact with GLU 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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124B MET* 3.7 29.6 - - + +
125B PRO 3.0 16.8 + - - +
126B LYS* 3.4 9.8 + - - +
128B PHE* 1.3 76.9 - - - +
130B SER* 1.3 56.4 + - - +
132B VAL* 3.3 4.4 + - - +
133B THR* 2.8 36.7 + - - +
139B VAL* 3.9 22.6 - - + +
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Residues in contact with SER 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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126B LYS 3.0 17.7 + - - -
127B SER* 3.6 7.4 - - - -
129B GLU* 1.3 76.8 - - - +
131B ALA* 1.3 60.2 + - - +
133B THR* 3.8 5.5 - - - -
134B ALA* 2.9 33.8 + - - +
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Residues in contact with ALA 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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127B SER 3.3 9.4 + - - +
128B PHE* 3.1 9.7 + - + +
130B SER* 1.3 81.2 - - - +
132B VAL* 1.3 61.0 + - - +
134B ALA* 4.0 5.3 - - - +
135B GLN* 3.2 24.9 + - - +
171B LEU* 3.7 13.8 - - + +
228B HIS* 4.0 26.0 - - + +
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Residues in contact with VAL 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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124B MET* 4.7 6.3 - - + -
128B PHE* 3.1 46.5 + - + +
129B GLU* 3.6 7.4 - - - +
130B SER 3.3 0.4 - - - -
131B ALA* 1.3 73.8 - - - +
133B THR* 1.3 59.8 + - - +
136B PHE* 2.8 35.1 + - + +
138B SER 4.6 0.2 - - - +
139B VAL* 4.1 19.1 - - + -
142B PHE* 3.4 39.9 - - + -
161B LEU* 4.9 5.8 - - + -
171B LEU* 4.2 10.1 - - + -
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Residues in contact with THR 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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129B GLU* 2.8 30.3 + - - +
130B SER* 3.8 6.7 - - - -
132B VAL* 1.3 75.8 - - - +
134B ALA* 1.3 57.3 + - - +
137B GLY* 2.8 49.1 + - - +
138B SER* 4.1 11.0 - - - +
139B VAL* 4.1 10.7 + - - +
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Residues in contact with ALA 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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130B SER* 2.9 20.4 + - - +
131B ALA* 4.0 5.2 - - - +
133B THR* 1.3 78.6 - - - +
135B GLN* 1.3 59.7 + - - +
137B GLY* 4.4 1.6 + - - -
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Residues in contact with GLN 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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131B ALA 3.2 16.8 + - - +
134B ALA* 1.3 80.6 - - - +
136B PHE* 1.3 92.0 + - + +
170B GLN* 3.3 17.5 - - - +
171B LEU* 3.2 38.9 + - + +
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Residues in contact with PHE 136 (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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132B VAL* 2.8 25.1 + - + +
135B GLN* 1.3 97.1 - - + +
137B GLY* 1.3 57.5 + - - +
138B SER 3.3 7.3 + - - +
141B GLN* 3.4 19.6 + - - +
142B PHE* 3.7 50.7 - + + +
145B ALA* 5.1 6.3 - - + -
161B LEU* 4.0 13.7 - - + -
171B LEU* 3.9 27.1 - - + -
172B VAL* 4.7 1.3 - - - -
173B ILE* 4.0 24.9 - - + -
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Residues in contact with GLY 137 (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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133B THR* 2.8 28.8 + - - +
134B ALA 4.4 1.3 + - - -
135B GLN 3.6 1.4 - - - -
136B PHE* 1.3 76.8 - - - +
138B SER* 1.3 59.5 + - - +
141B GLN* 3.3 11.2 - - - +
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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