Contacts of the helix formed by residues 114 - 129 (chain B) in PDB entry 5I1U
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 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 1.3 83.5 - - - +
115B PRO* 1.3 76.6 - - - +
116B SER* 3.6 7.2 + - - -
117B GLU* 3.1 36.5 + - - +
118B ARG* 2.9 22.3 + - - +
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B HIS* 4.9 1.6 + - - -
35B GLU* 3.5 41.1 - - + +
36B LEU* 3.8 32.7 - - + +
113B THR 4.5 1.1 - - - +
114B SER* 1.3 87.9 - - - +
116B SER* 1.3 63.3 + - - +
118B ARG* 3.4 8.5 + - + +
119B ALA* 3.1 24.4 + - - +
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Residues in contact with SER 116 (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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36B LEU* 3.9 16.4 - - - +
75B PHE* 3.6 11.0 - - - -
79B PHE* 3.5 24.3 - - - -
82B GLN* 3.1 25.9 + - - -
97B ILE* 5.9 1.1 - - - -
101B LEU* 4.2 8.3 - - - -
114B SER* 3.3 7.2 + - - -
115B PRO* 1.3 79.6 - - - +
117B GLU* 1.3 59.3 + - - +
119B ALA* 3.4 0.8 + - - -
120B PHE* 2.9 31.9 + - - +
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Residues in contact with GLU 117 (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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97B ILE* 4.8 3.8 - - - +
100B ARG* 2.7 47.8 + - + +
101B LEU* 4.1 15.4 - - + +
104B ILE* 3.9 20.5 - - + +
109B LEU* 4.2 5.6 - - + -
111B ALA 3.9 0.3 - - - +
112B VAL* 3.2 21.0 - - + +
113B THR* 2.8 22.5 + - - -
114B SER* 3.1 29.7 + - - +
116B SER* 1.3 74.3 - - - +
118B ARG* 1.3 60.6 + - - +
121B ALA* 2.9 26.5 + - - +
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Residues in contact with ARG 118 (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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32B ARG* 4.0 30.2 + - - +
33B HIS* 3.7 23.3 + - + +
112B VAL* 3.4 14.9 - - + +
113B THR 5.5 2.2 - - - +
114B SER 2.9 16.2 + - - +
115B PRO* 3.8 7.4 - - + +
117B GLU* 1.3 76.2 - - - +
119B ALA* 1.3 62.5 + - - +
121B ALA* 4.0 2.3 - - - +
122B ASP* 3.3 22.0 + - - +
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Residues in contact with ALA 119 (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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29B TRP* 3.9 16.7 - - + -
33B HIS* 3.7 17.5 + - - +
36B LEU* 3.6 25.8 - - + -
75B PHE* 4.0 4.7 - - + -
115B PRO 3.1 17.4 + - - +
116B SER 3.8 2.9 - - - +
118B ARG* 1.3 75.4 - - - +
120B PHE* 1.3 65.5 + - - +
122B ASP* 3.3 5.9 + - - +
123B LEU* 3.0 26.7 + - - +
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Residues in contact with PHE 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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75B PHE* 3.9 14.1 - + + -
101B LEU* 3.7 38.6 - - + -
104B ILE* 3.6 26.7 - - + -
105B ALA* 3.9 13.5 - - + -
116B SER 2.9 17.8 + - - +
117B GLU 4.0 1.3 - - - +
119B ALA* 1.3 78.0 - - - +
121B ALA* 1.3 55.8 + - - +
123B LEU* 3.1 8.2 + - + -
124B TRP* 2.7 49.9 + + + +
143B TRP* 3.5 56.5 - + - -
147B PHE* 3.8 12.8 - + - -
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Residues in contact with ALA 121 (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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104B ILE* 4.0 18.6 - - + +
112B VAL* 4.1 23.6 - - + -
117B GLU 2.9 22.4 + - - +
118B ARG* 4.0 3.8 - - - +
120B PHE* 1.3 74.1 - - - +
122B ASP* 1.3 62.5 + - - +
124B TRP* 4.1 1.3 - - - +
125B ARG* 3.1 25.5 + - - +
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Residues in contact with ASP 122 (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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29B TRP* 2.9 28.5 + - - -
32B ARG* 5.0 5.5 + - - -
33B HIS* 4.3 12.8 - - + +
118B ARG 3.3 11.0 + - - +
119B ALA 3.3 9.8 + - - +
120B PHE 3.2 0.4 - - - -
121B ALA* 1.3 79.8 - - - +
123B LEU* 1.3 63.4 + - - +
125B ARG* 3.4 4.5 + - - +
126B ARG* 2.9 51.6 + - - +
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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
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29B TRP* 4.1 8.5 - - + -
68B LEU* 4.0 15.7 - - + +
71B ASP* 3.7 31.4 - - + +
72B LEU* 3.8 18.6 - - + +
75B PHE* 3.4 43.7 - - + -
119B ALA 3.0 17.0 + - - +
120B PHE* 3.7 11.9 - - + +
122B ASP* 1.3 77.5 - - - +
124B TRP* 1.3 53.7 + - - +
126B ARG* 3.2 12.4 + - - +
127B ILE* 2.8 48.6 + - + +
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Residues in contact with TRP 124 (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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104B ILE* 3.6 21.6 + - + -
105B ALA* 3.1 32.3 + - + +
107B GLY 5.3 0.4 - - - +
120B PHE* 2.7 37.9 + + + +
121B ALA* 4.1 4.0 - - - +
123B LEU* 1.3 71.1 - - - +
125B ARG* 1.3 66.6 + - - +
127B ILE* 4.0 21.3 - - + +
128B THR* 3.0 49.9 + - + +
136B ARG* 4.1 13.5 - - + +
139B ALA* 3.9 11.9 - - + -
140B ALA* 3.6 28.5 - - + -
143B TRP* 3.6 34.5 - + - -
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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
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121B ALA 3.1 19.1 + - - +
122B ASP* 3.7 6.3 - - - +
124B TRP* 1.3 76.7 - - - +
126B ARG* 1.3 67.5 + - + +
128B THR* 2.9 33.6 + - - -
129B LEU* 3.3 52.0 + - + +
136B ARG* 4.2 14.4 - - - +
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Residues in contact with ARG 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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29B TRP* 3.4 10.3 - - - +
32B ARG* 5.6 0.6 - - - +
64B GLU 4.8 2.2 + - - -
67B ALA* 4.1 4.9 - - - +
68B LEU* 3.4 45.8 - - + +
71B ASP* 2.9 33.3 + - - +
122B ASP* 2.9 47.4 + - - +
123B LEU* 3.6 8.8 - - - +
125B ARG* 1.3 80.7 - - + +
127B ILE* 1.3 62.1 + - - +
128B THR 3.4 0.5 + - - -
129B LEU* 3.5 17.9 + - + +
187B ARG* 3.0 27.3 + - - +
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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
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68B LEU* 4.4 14.8 - - + -
72B LEU* 4.6 8.1 - - + -
123B LEU* 2.8 34.5 + - + +
124B TRP* 3.3 22.4 + - + +
126B ARG* 1.3 73.5 - - - +
128B THR* 1.3 59.8 + - - +
131B MET* 3.7 5.4 - - - +
135B TRP* 3.7 13.6 - - + -
139B ALA* 5.3 0.2 - - + -
143B TRP* 4.2 29.4 - - + +
184B MET* 3.4 43.1 - - + -
187B ARG* 3.0 29.7 + - - +
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Residues in contact with THR 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 TRP* 3.0 62.8 + - + +
125B ARG* 2.9 29.9 + - - -
127B ILE* 1.3 76.1 - - + +
129B LEU* 1.3 64.9 + - - +
130B GLY 3.2 0.5 + - - -
131B MET* 3.1 22.0 + - - +
135B TRP* 4.7 2.2 - - + -
136B ARG* 3.6 39.2 + - + +
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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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125B ARG* 3.3 50.6 + - + +
126B ARG* 3.7 17.9 - - + +
127B ILE 3.4 1.2 - - - -
128B THR* 1.3 78.5 + - - +
130B GLY* 1.3 59.5 + - - +
131B MET* 3.4 7.4 + - - +
187B ARG* 3.4 23.1 + - - +
190B HIS* 5.9 0.3 - - - -
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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
------------------------------------------------------------
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