Contacts of the helix formed by residues 123 - 138 (chain B) in PDB entry 3H8E
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 HIS 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ASP* 4.1 17.5 + - - -
121B ASP* 3.2 3.5 + - + +
122B ALA* 1.3 99.0 + - + +
124B TYR* 1.3 64.0 + - - +
127B TYR* 3.2 25.6 - - - +
161B ALA* 4.7 2.8 - - + +
162B ASP* 3.2 30.7 + - - -
164B ALA* 4.9 1.8 - - - +
165B GLY* 3.5 25.9 + - - +
168B GLU* 3.6 23.6 - - + -
169B VAL* 3.5 20.6 - - + +
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 2.9 23.7 + - - +
123B HIS* 1.3 74.5 - - - +
125B GLY* 1.3 64.3 + - - +
127B TYR 3.3 1.4 + - - -
128B ARG* 2.8 62.9 + - + +
168B GLU* 3.7 16.1 - - + +
171B ARG* 3.5 42.2 + - - +
172B ALA* 3.4 40.9 - - + +
175B HIS* 2.5 30.3 + - - -
489B GLN* 5.1 2.0 + - - -
492B LEU* 4.5 1.9 - - - +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 3.8 27.0 - - - -
121B ASP* 2.7 18.6 + - - -
124B TYR* 1.3 81.3 - - - +
126B LYS* 1.3 61.6 + - - +
127B TYR 3.3 0.3 + - - -
128B ARG* 3.3 13.8 + - - +
129B LEU* 3.4 17.8 + - - +
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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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89B TRP* 2.9 58.3 + - + +
112B LEU 2.8 25.7 + - - -
113B ASP* 3.1 19.8 + - - +
115B VAL 2.7 29.3 + - - +
117B VAL* 3.9 12.8 - - + +
120B ARG* 3.9 10.1 - - + +
121B ASP 3.2 18.9 + - - +
122B ALA* 3.6 25.2 + - - +
125B GLY* 1.3 77.0 - - - +
127B TYR* 1.3 74.6 + - + +
129B LEU* 3.4 1.0 + - - +
130B LEU* 3.2 10.7 + - - +
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Residues in contact with TYR 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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110B LEU* 5.5 2.3 + - + -
112B LEU* 3.8 5.7 + - + +
113B ASP* 3.8 25.2 + - - -
122B ALA 3.3 21.5 - - - -
123B HIS* 3.2 26.0 + - - +
124B TYR 3.3 2.2 + - - -
125B GLY 3.3 0.2 - - - -
126B LYS* 1.3 101.7 + - + +
128B ARG* 1.3 61.4 - - - +
129B LEU 3.2 1.3 - - - -
130B LEU* 3.8 29.4 - - + +
131B ALA* 2.8 32.2 + - - +
159B LEU* 3.8 35.0 - - + -
160B LEU 4.0 12.3 + - - -
161B ALA* 5.4 1.8 - - + -
169B VAL* 3.7 25.4 - - + -
172B ALA* 3.8 10.5 - - + -
173B VAL* 5.4 1.1 - - + -
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Residues in contact with ARG 128 (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 TYR* 2.8 73.6 + - + +
125B GLY* 3.6 9.9 - - - +
127B TYR* 1.3 76.8 - - - +
129B LEU* 1.3 66.3 + - + +
132B GLU* 3.1 40.1 + - - +
172B ALA* 3.5 15.1 - - + +
175B HIS* 3.7 17.0 - - - -
176B ALA* 3.8 6.9 - - - +
179B ILE* 3.5 31.6 - - - +
409B ARG 4.7 3.9 + - - +
410B ALA* 4.0 20.6 + - - +
489B GLN* 2.8 35.7 + - - +
492B LEU* 4.4 4.4 - - - +
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Residues in contact with LEU 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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86B ASP* 3.4 43.7 - - + +
89B TRP* 3.9 14.8 - - + -
90B ARG* 3.7 31.3 + - + +
120B ARG* 3.5 27.4 - - - +
125B GLY 3.4 11.3 + - - +
126B LYS* 3.7 8.1 - - - +
127B TYR 3.2 0.6 - - - -
128B ARG* 1.3 84.7 - - + +
130B LEU* 1.3 68.4 + - - +
132B GLU* 5.2 2.5 - - - +
133B THR* 3.0 29.2 + - - -
409B ARG 4.4 4.5 - - - +
410B ALA* 4.7 4.9 - - - +
411B ASP* 4.3 10.5 - - + -
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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
----------------------------------------------------------
89B TRP* 3.5 39.8 - - + +
90B ARG* 5.9 0.2 - - - -
93B VAL* 3.7 30.3 - - + +
110B LEU* 4.4 13.2 - - + -
112B LEU* 4.1 14.8 - - + -
126B LYS 3.2 8.0 + - - +
127B TYR* 3.9 20.9 - - + +
128B ARG 3.4 0.2 - - - -
129B LEU* 1.3 81.3 - - - +
131B ALA* 1.3 65.1 + - - +
134B LEU* 2.9 33.7 + - + +
159B LEU* 3.8 31.4 - - + -
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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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3B LEU* 3.6 27.6 - - + -
127B TYR 2.8 22.3 + - - +
130B LEU* 1.3 80.8 - - + +
132B GLU* 1.3 60.9 - - - +
134B LEU* 3.4 3.3 + - - +
135B LEU* 2.9 34.9 + - + +
159B LEU* 5.1 0.4 - - + -
173B VAL* 4.3 9.9 - - + -
176B ALA* 3.4 19.7 - - + -
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Residues in contact with GLU 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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90B ARG* 3.6 22.7 + - - +
128B ARG* 3.1 27.0 + - - +
129B LEU* 5.2 1.7 - - - +
131B ALA* 1.3 77.6 - - - +
133B THR* 1.3 56.3 + - - +
135B LEU* 4.6 1.8 - - - +
136B ASP* 2.9 38.5 + - + +
176B ALA* 3.5 17.3 - - + +
179B ILE* 3.3 19.8 - - + +
180B ALA* 4.9 2.0 - - + -
183B MET* 3.3 20.7 - - + +
410B ALA 4.5 9.8 - - - +
485B PRO* 3.0 32.7 - - - +
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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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90B ARG* 2.7 64.1 + - + +
93B VAL* 4.0 8.5 - - + -
94B ALA* 4.0 21.8 - - + +
129B LEU 3.0 12.3 + - - -
130B LEU 3.8 2.7 - - - -
132B GLU* 1.3 76.1 - - - +
134B LEU* 1.3 64.6 + - - +
136B ASP* 4.5 1.7 - - - +
137B GLY* 3.0 22.0 + - - -
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Residues in contact with LEU 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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1B MET* 3.9 24.2 - - + -
3B LEU* 3.9 27.8 - - + -
93B VAL* 4.3 10.7 - - + +
97B ALA* 4.0 27.4 - - + -
100B LEU* 5.7 3.1 - - + -
101B LYS* 5.6 0.7 - - - -
110B LEU* 4.4 13.5 - - + -
130B LEU* 2.9 22.0 + - + +
131B ALA 3.7 4.3 - - - +
133B THR* 1.3 80.3 - - - +
135B LEU* 1.3 63.6 + - + +
137B GLY* 3.4 6.9 + - - -
138B GLU* 3.5 17.4 + - - +
154B LEU* 5.4 2.7 - - + -
157B VAL* 3.9 25.8 - - + -
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Residues in contact with LEU 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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1B MET* 4.1 42.2 - - + +
3B LEU* 4.1 24.0 - - + -
131B ALA 2.9 20.8 + - - +
134B LEU* 1.3 78.9 - - + +
136B ASP* 1.3 64.3 + - - +
138B GLU* 3.2 21.4 + - + +
139B TYR* 4.1 1.6 + - - -
176B ALA 4.3 2.0 - - - +
177B SER* 3.2 43.7 - - - +
180B ALA* 3.6 16.1 - - + +
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Residues in contact with ASP 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 GLU* 2.9 20.7 + - + +
133B THR* 4.5 2.2 - - - +
135B LEU* 1.3 77.0 - - - +
137B GLY* 1.3 56.9 + - - +
138B GLU 3.1 0.2 - - - -
139B TYR* 3.1 30.0 + - - +
180B ALA* 4.0 14.5 - - + +
183B MET* 3.7 35.1 - - + +
184B ALA* 5.1 0.7 + - - +
187B ARG* 2.8 39.3 + - - -
481B GLY 5.4 0.3 + - - -
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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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101B LYS* 2.8 27.5 + - - -
133B THR 3.0 20.6 + - - -
134B LEU 3.7 4.0 - - - -
135B LEU 3.1 0.4 - - - -
136B ASP* 1.3 77.7 + - - +
138B GLU* 1.3 59.6 + - - +
139B TYR 3.2 4.2 + - - +
152B ARG* 5.0 0.7 + - - -
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Residues in contact with GLU 138 (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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1B MET* 3.1 52.0 + - + +
101B LYS* 3.1 31.6 - - - +
134B LEU* 3.5 15.0 - - - +
135B LEU* 3.3 13.7 - - + +
136B ASP 3.1 0.6 - - - -
137B GLY* 1.3 76.6 - - - +
139B TYR* 1.4 65.0 + - - +
140B VAL* 3.3 5.0 + - - +
152B ARG* 2.9 37.0 + - - +
154B LEU* 4.4 7.0 - - - +
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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