Contacts of the helix formed by residues 117 - 137 (chain B) in PDB entry 3I59
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 6.6 0.4 - - + -
113B ILE* 3.3 19.3 - - + +
114B ALA 4.2 6.3 - - - +
115B ASP 3.5 9.6 - - - +
116B ARG* 1.3 86.0 - - - +
118B GLU* 1.3 69.9 + - - +
119B ILE 3.0 1.7 + - - -
120B SER* 3.1 21.9 + - - +
121B GLU* 4.2 5.6 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 6.4 2.7 - - - -
15B GLU* 4.7 16.1 - - + +
116B ARG* 3.5 26.3 - - + +
117B PRO* 1.3 84.7 - - - +
119B ILE* 1.3 65.5 + - + +
120B SER 3.2 0.4 - - - -
121B GLU* 3.4 29.9 + - - +
122B GLN* 3.4 19.0 + - + +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.8 39.0 - - + +
11B PHE* 4.0 13.5 - - + -
109B LEU* 4.7 3.8 - - + -
112B TRP* 3.6 34.8 - - + +
113B ILE* 3.6 19.1 - - + -
116B ARG* 2.9 33.8 + - + +
118B GLU* 1.3 78.2 - - + +
120B SER* 1.3 64.1 + - - +
122B GLN* 3.3 2.9 + - - +
123B LEU* 3.1 30.8 + - + +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 5.8 0.2 - - - -
117A PRO* 5.0 1.9 - - - +
120A SER* 3.5 33.2 - - - -
121A GLU* 6.2 0.2 - - - +
124A LEU* 4.6 4.1 - - - +
113B ILE* 3.2 35.6 - - - +
117B PRO 3.1 12.0 + - - -
119B ILE* 1.3 79.5 - - - +
121B GLU* 1.3 63.1 + - - +
123B LEU* 3.3 6.2 + - - +
124B LEU* 3.0 29.0 + - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 5.0 0.7 - - - +
110A ARG* 3.6 39.7 + - + +
113A ILE* 5.0 16.8 - - + +
117B PRO 4.5 7.4 - - - +
118B GLU* 3.4 22.5 + - - +
119B ILE 3.4 0.2 - - - -
120B SER* 1.3 78.9 - - - +
122B GLN* 1.3 69.3 + - - +
124B LEU* 3.3 12.5 + - + +
125B ARG* 2.8 29.6 + - - +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY 3.6 13.7 - - - +
10B ILE 3.7 20.6 - - - +
11B PHE 5.1 0.2 - - - -
12B GLN* 3.4 33.1 + - - +
118B GLU* 3.4 13.8 + - + +
119B ILE 3.3 4.6 + - - +
120B SER 3.3 1.0 - - - -
121B GLU* 1.3 86.3 + - - +
123B LEU* 1.3 53.7 + - - +
125B ARG* 2.8 42.9 + - - +
126B VAL* 2.7 41.8 + - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.7 24.5 - - + -
10B ILE* 3.9 27.4 - - + -
47B LEU* 5.7 0.7 - - + -
77B MET* 4.3 21.1 - - + -
84B PHE* 4.0 28.7 - - + -
109B LEU* 4.1 17.9 - - + -
113B ILE* 4.1 6.7 - - + -
119B ILE* 3.1 34.5 + - + +
120B SER 3.7 3.8 - - - +
122B GLN* 1.3 73.7 - - - +
124B LEU* 1.3 64.9 + - - +
126B VAL* 3.1 4.7 + - + +
127B LEU* 2.9 30.1 + - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.2 33.2 - - + -
113A ILE* 4.3 11.9 - - + -
120A SER* 4.1 21.3 - - - +
123A LEU* 3.9 14.6 - - + -
124A LEU* 3.4 42.0 - - + +
127A LEU* 3.8 14.4 - - + +
120B SER 3.0 22.2 + - - +
121B GLU* 3.6 10.5 - - + +
123B LEU* 1.3 74.7 - - - +
125B ARG* 1.3 64.5 + - - +
127B LEU 3.5 0.2 + - - -
128B ALA* 2.9 27.0 + - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.4 25.0 + - - +
85A ASP* 3.9 16.4 + - - +
86A PRO* 5.5 3.4 - - - -
9B GLY* 3.1 30.3 + - - -
12B GLN* 3.9 13.8 - - - +
121B GLU 2.8 17.4 + - - +
122B GLN* 2.8 35.0 + - - +
124B LEU* 1.3 77.4 - - - +
126B VAL* 1.3 67.4 + - - +
128B ALA* 3.8 0.3 - - - +
129B ARG* 2.9 61.5 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 4.0 20.4 - - - -
10B ILE* 4.5 1.6 - - - +
77B MET* 4.3 23.6 - - + -
122B GLN 2.7 32.1 + - - +
123B LEU* 3.1 8.7 + - + +
125B ARG* 1.3 94.5 - - - +
127B LEU* 1.3 68.8 + - + +
129B ARG* 3.5 13.2 + - - +
130B ARG* 3.1 43.8 + - + +
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Residues in contact with LEU 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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124A LEU* 4.0 22.7 - - + +
127A LEU* 4.1 13.5 - - + -
128A ALA* 4.0 16.8 - - + +
131A LEU* 3.8 18.0 - - + +
77B MET* 5.2 1.8 - - + -
80B GLU* 4.0 27.8 - - + +
81B LEU* 4.6 1.6 - - + -
84B PHE* 3.7 29.6 - - + -
123B LEU* 2.9 20.7 + - + +
126B VAL* 1.3 85.3 - - + +
128B ALA* 1.3 66.1 + - - +
130B ARG* 3.0 10.2 + - - +
131B LEU* 3.0 26.1 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.9 26.4 - - + +
84A PHE* 3.7 22.0 - - + -
85A ASP* 3.7 16.6 - - + +
127A LEU* 4.1 7.3 - - + +
124B LEU 2.9 19.5 + - - +
127B LEU* 1.3 75.7 - - - +
129B ARG* 1.3 59.7 + - - +
131B LEU* 3.0 6.8 + - - +
132B ARG* 2.9 27.0 + - - +
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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
----------------------------------------------------------
85A ASP* 3.3 27.8 + - - +
9B GLY* 6.3 1.2 - - - -
125B ARG* 2.9 44.0 + - - +
126B VAL* 3.6 13.0 + - - +
128B ALA* 1.3 76.7 - - - +
130B ARG* 1.3 59.3 + - - +
132B ARG* 3.7 4.5 - - + +
133B ARG* 3.0 60.0 + - + +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.3 19.0 - - + +
72B MET* 4.1 15.2 - - - +
76B ASP* 5.6 1.0 - - - +
77B MET* 3.3 33.5 + - - +
80B GLU* 3.2 32.9 + - - -
126B VAL* 3.1 36.2 + - + +
127B LEU* 3.0 15.3 + - - +
129B ARG* 1.3 77.2 - - + +
131B LEU* 1.3 62.4 + - - +
133B ARG* 4.1 8.8 - - - +
134B THR* 2.8 29.1 + - - -
301B N6S 4.1 18.9 + - + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.0 20.6 - - + -
127A LEU* 3.9 44.2 - - + +
130A ARG* 4.4 11.9 - - + -
131A LEU* 3.2 28.9 - - + +
134A THR* 3.8 19.5 - - + +
301A N6R 4.6 15.0 + - + +
127B LEU 3.0 22.1 + - - +
128B ALA 3.0 6.5 + - - +
130B ARG* 1.3 75.6 - - - +
132B ARG* 1.3 67.2 + - - +
134B THR* 3.2 5.3 + - - +
135B ASN* 3.1 24.9 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.2 6.9 + - + +
82A SER* 3.8 13.7 + - - +
85A ASP* 2.2 63.5 + - - +
86A PRO 4.1 2.0 + - - -
87A GLY* 3.3 21.3 + - - +
88A PRO* 2.9 32.4 + - - +
90A THR* 3.6 32.2 - - + +
128B ALA 2.9 15.2 + - - +
129B ARG* 3.7 7.4 - - - +
131B LEU* 1.3 77.5 - - - +
133B ARG* 1.3 66.1 + - + +
135B ASN* 3.2 7.9 + - - +
136B ASN* 3.1 35.5 + - - +
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Residues in contact with ARG 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 ARG* 3.0 50.1 + - + +
130B ARG* 4.1 9.4 - - - +
132B ARG* 1.3 79.2 - - + +
134B THR* 1.3 61.7 + - - +
136B ASN* 3.2 21.3 + - - +
137B ASN* 3.2 14.8 + - - +
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Residues in contact with THR 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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131A LEU* 4.9 2.8 - - - +
134A THR* 3.7 30.6 - - + +
138A LEU* 3.9 10.0 - - + +
301A N6R 4.1 6.5 - - + -
130B ARG 2.8 21.0 + - - -
131B LEU* 3.2 7.3 + - - -
133B ARG* 1.3 76.5 - - - +
135B ASN* 1.3 64.5 + - - +
137B ASN* 3.1 22.2 + - - +
138B LEU* 5.3 0.2 - - - -
301B N6S 3.4 43.4 - - + +
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Residues in contact with ASN 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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59A ARG* 3.3 44.9 + - - +
69A LEU* 4.1 2.8 - - - +
90A THR* 3.6 8.5 + - - +
301A N6R 2.7 71.4 + - - +
131B LEU 3.1 12.0 + - - +
132B ARG* 3.2 12.1 + - - +
134B THR* 1.3 76.8 - - - +
136B ASN* 1.3 63.2 + - - +
137B ASN 3.0 1.7 + - - -
138B LEU* 3.8 12.5 + - - +
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Residues in contact with ASN 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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59A ARG* 2.8 33.1 + - - +
90A THR* 5.8 0.2 - - - +
132B ARG* 3.1 28.8 + - - +
133B ARG* 3.2 12.7 + - - +
135B ASN* 1.3 74.3 - - - +
137B ASN* 1.3 57.7 + - - +
138B LEU 3.5 4.0 + - - -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 5.7 1.4 - - - +
133B ARG 3.2 12.2 + - - +
134B THR* 3.1 12.9 + - - +
135B ASN 3.0 2.6 + - - -
136B ASN* 1.3 77.5 - - + +
138B LEU* 1.3 58.3 + - - +
139B ALA* 3.3 11.5 + - + +
140B ASP* 4.7 2.6 + - - +
301B N6S 3.7 31.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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