Contacts of the helix formed by residues 119 - 136 (chain B) in PDB entry 4R8U
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 SER 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B HIS 3.9 0.8 + - - -
116B CYS* 3.1 15.3 + - - +
117B HIS* 3.2 3.3 - - - -
118B GLY* 1.3 74.4 - - - +
120B ALA* 1.3 63.5 + - - +
121B THR* 3.5 9.5 + - - -
122B LEU* 3.3 33.6 + - - +
123B ILE* 2.9 26.3 + - - +
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Residues in contact with ALA 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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4B LYS* 4.1 19.3 - - + +
6B ILE* 3.6 8.1 - - + +
110B VAL* 4.0 23.6 - - + -
118B GLY 3.5 5.9 + - - -
119B SER* 1.3 71.8 + - - +
121B THR* 1.3 63.1 + - - +
123B ILE* 4.3 6.9 - - - +
124B ALA* 2.9 25.5 + - - +
143B VAL* 3.6 25.8 - - + -
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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
----------------------------------------------------------
119B SER* 3.1 8.8 + - - -
120B ALA* 1.3 78.6 - - - +
122B LEU* 1.3 68.5 + - + +
124B ALA 3.4 0.3 + - - -
125B GLN* 3.1 24.7 + - + +
143B VAL* 4.6 6.2 - - - +
162B GLN* 3.2 24.9 + - - +
164B VAL* 3.4 28.8 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B CYS* 3.8 23.3 - - + +
117B HIS* 4.9 9.6 - - + -
119B SER* 3.0 28.5 + - - +
121B THR* 1.3 83.5 - - + +
123B ILE* 1.3 60.8 + - - +
125B GLN* 3.5 11.3 + - + +
126B GLU* 2.9 31.8 + - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.0 11.0 - - + -
94B TYR* 4.2 15.3 - - + -
110B VAL* 4.2 22.2 - - + +
113B SER* 3.3 33.4 - - - +
115B HIS* 3.9 21.8 - - + +
116B CYS* 4.0 13.5 - - - -
118B GLY 5.3 0.9 - - - -
119B SER 2.9 21.7 + - - +
120B ALA 3.7 4.3 - - - +
122B LEU* 1.3 77.6 - - - +
124B ALA* 1.3 56.9 + - - +
126B GLU* 3.1 3.4 + - - +
127B ILE* 2.8 53.7 + - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.9 13.7 - - + +
8B VAL* 5.9 0.6 - - - +
120B ALA 2.9 18.7 + - - +
121B THR 3.7 2.5 - - - +
123B ILE* 1.3 75.3 - - - +
125B GLN* 1.3 58.2 + - - +
127B ILE* 3.2 7.1 + - - +
128B ARG* 2.9 34.1 + - - +
141B ALA* 4.1 15.3 - - + -
143B VAL* 3.9 19.7 - - + -
162B GLN* 3.5 14.1 - - - +
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Residues in contact with GLN 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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121B THR* 3.1 18.1 + - + +
122B LEU* 3.7 12.8 - - + +
124B ALA* 1.3 74.0 - - - +
126B GLU* 1.3 58.2 + - - +
128B ARG* 2.8 33.6 + - - +
129B GLN* 3.0 33.6 + - + +
162B GLN* 3.0 17.9 + - - +
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Residues in contact with GLU 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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94B TYR* 3.2 30.2 + - + +
116B CYS* 3.1 26.7 - - - -
122B LEU* 2.9 15.4 + - - +
123B ILE* 3.1 6.0 + - - +
125B GLN* 1.3 73.6 - - - +
127B ILE* 1.3 60.5 + - - +
129B GLN* 3.3 5.4 + - + +
130B THR* 2.9 38.1 + - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 5.0 2.2 - - + -
8B VAL* 4.6 10.8 - - + -
90B ILE* 4.5 3.6 - - + -
91B PHE* 3.4 32.3 - - + -
94B TYR* 3.7 34.8 - - + -
108B LEU* 3.6 28.9 - - + -
123B ILE* 2.8 35.8 + - + +
124B ALA* 3.6 7.9 - - - +
126B GLU* 1.3 77.2 - - - +
128B ARG* 1.3 63.3 + - - +
130B THR* 3.5 3.4 + - - -
131B ILE* 3.1 34.7 + - + +
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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
----------------------------------------------------------
8B VAL* 5.2 4.7 - - + -
124B ALA 2.9 14.4 + - - +
125B GLN* 2.8 39.2 + - - +
127B ILE* 1.3 77.4 - - + +
129B GLN* 1.3 61.9 + - - +
131B ILE* 3.4 10.6 + - - +
132B PHE* 3.2 21.5 + - - +
137B LEU 5.0 0.5 - - - +
138B THR* 5.8 0.2 - - - -
139B ALA* 3.0 34.7 + - + +
140B SER 4.7 0.2 - - - -
141B ALA* 3.7 26.0 - - + +
160B ASN* 3.2 42.2 + - - +
161B GLY* 3.4 10.3 + - - +
162B GLN* 3.1 25.9 + - - +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 3.0 22.0 + - + +
126B GLU* 3.7 6.7 - - + +
127B ILE 3.2 0.2 - - - -
128B ARG* 1.3 74.5 - - - +
130B THR* 1.3 65.1 + - - +
132B PHE* 3.3 16.1 + - - +
133B ASN* 2.9 65.1 + - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.7 19.5 - - + -
93B ARG* 3.6 28.0 - - - +
94B TYR* 3.7 15.0 + - + +
126B GLU* 2.9 20.6 + - - +
127B ILE* 3.7 4.9 - - - -
129B GLN* 1.3 77.0 - - - +
131B ILE* 1.3 57.3 + - - +
133B ASN* 3.2 8.2 + - + +
134B GLU* 2.9 40.6 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.5 1.8 - - + -
10B MET* 4.1 21.1 - - + -
87B ILE* 4.1 15.9 - - + -
90B ILE* 3.9 24.5 - - + -
91B PHE* 4.0 27.8 - - + -
127B ILE* 3.1 19.3 + - + +
128B ARG* 3.5 8.7 - - - +
129B GLN 3.3 0.2 - - - -
130B THR* 1.3 75.6 - - - +
132B PHE* 1.3 57.7 + - - +
135B LEU* 3.0 39.3 + - + +
137B LEU 3.5 15.2 - - - +
139B ALA* 4.3 19.1 - - + -
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Residues in contact with PHE 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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128B ARG 3.2 13.0 + - - +
129B GLN* 3.7 19.5 - - - +
130B THR 3.3 0.2 - - - -
131B ILE* 1.3 74.5 - - - +
133B ASN* 1.3 73.2 + - - +
136B GLN* 3.0 39.7 + - + +
137B LEU 3.4 11.0 + - - +
138B THR* 3.9 29.6 - - + -
160B ASN* 6.0 2.0 - - - +
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Residues in contact with ASN 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 GLN* 2.9 50.8 + - - +
130B THR* 3.7 6.9 - - - +
132B PHE* 1.3 87.3 - - - +
134B GLU* 1.3 64.5 + - + +
136B GLN* 4.4 6.9 + - - +
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Residues in contact with GLU 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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86B HIS* 2.9 34.5 + - + -
90B ILE* 3.7 3.5 - - - +
93B ARG* 2.7 46.6 + - - -
130B THR* 2.9 30.2 + - + +
133B ASN* 1.3 77.9 - - + +
135B LEU* 1.3 63.5 + - + +
136B GLN* 5.1 2.7 + - - +
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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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20B ARG* 2.9 30.4 + - - +
83B ALA* 3.7 23.3 - - + +
86B HIS* 3.3 39.0 - - + +
87B ILE* 3.5 32.5 - - + +
90B ILE* 3.7 22.9 - - + -
131B ILE* 3.0 22.9 + - + +
134B GLU* 1.3 76.2 - - + +
136B GLN* 1.3 74.9 + - - +
137B LEU* 3.2 13.9 + - + +
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Residues in contact with GLN 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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20B ARG* 3.9 27.2 - - + +
26B ARG* 5.0 6.9 + - - -
131B ILE 3.6 0.2 + - - -
132B PHE* 3.0 34.8 + - + +
133B ASN 4.7 6.3 - - - +
134B GLU 5.1 1.7 + - - -
135B LEU* 1.3 81.8 + - - +
137B LEU* 1.3 64.4 - - - +
138B THR* 5.6 0.7 - - - +
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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