Contacts of the helix formed by residues 119 - 135 (chain B) in PDB entry 5UQ3
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 THR 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.9 14.7 - - - +
108B PHE* 5.1 0.4 - - - -
116B SER 5.1 5.6 - - - +
117B GLU* 3.7 4.7 + - - +
118B HIS* 1.3 76.0 - - - +
120B ARG* 1.3 75.6 + - - +
121B ILE* 3.7 16.3 + - + +
122B ASN* 3.5 27.0 - - + +
123B PHE* 3.1 23.6 + - - +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 2.4 47.3 + - - +
81B ASP* 4.5 3.4 - - - +
82B LEU* 3.7 37.9 - - - +
83B ILE* 4.6 17.2 - - + +
119B THR* 1.3 82.5 + - - +
121B ILE* 1.3 61.4 + - - +
123B PHE* 3.2 7.0 + - - +
124B PHE* 3.1 37.4 + - + -
147B TRP 6.0 0.4 - - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 3.7 18.6 - - + +
120B ARG* 1.3 77.4 - - - +
122B ASN* 1.3 68.8 + - - +
124B PHE* 3.9 4.2 - - - -
125B ILE* 2.9 37.1 + - + +
148B ALA* 5.0 6.3 - - + +
149B LEU* 4.8 9.6 - - + -
160B PHE* 3.7 33.7 - - + -
163B LEU* 4.4 21.8 - - + -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.0 21.9 - - + -
113B PHE* 3.2 32.8 - - + -
117B GLU* 3.7 27.4 + - - +
119B THR* 3.5 21.3 + - + +
120B ARG 3.3 0.6 - - - -
121B ILE* 1.3 89.0 - - - +
123B PHE* 1.3 58.6 + - - +
125B ILE* 3.2 23.0 - - - +
126B ALA* 3.7 1.7 + - - +
167B LEU* 5.5 0.8 - - - +
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.4 19.5 - - + -
78B PHE* 4.3 16.2 - + - -
83B ILE* 3.6 24.9 - - + -
86B PHE* 4.7 5.4 - + - -
87B LEU* 5.2 1.1 - - + -
101B LEU* 3.5 24.9 - - + -
104B THR* 3.4 40.4 + - + -
108B PHE* 3.6 11.6 - + + -
119B THR 3.1 13.9 + - - +
120B ARG* 3.4 7.4 - - - +
121B ILE 3.1 0.4 - - - -
122B ASN* 1.3 75.3 - - - +
124B PHE* 1.3 105.7 + + - +
125B ILE 3.1 1.1 - - - -
126B ALA 2.9 12.1 + - - -
127B LEU* 2.9 23.7 + - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 4.8 7.0 - - + -
83B ILE* 3.8 19.3 - - + -
86B PHE* 3.7 34.8 - + + -
120B ARG* 3.1 28.1 + - + +
121B ILE 4.1 2.9 - - - +
123B PHE* 1.3 105.7 - + - +
125B ILE* 1.3 56.3 + - - +
127B LEU* 3.6 6.6 - - + +
128B TYR* 2.9 32.4 + - - +
144B ILE* 3.7 23.7 - - + +
147B TRP* 4.1 13.0 - - + -
148B ALA* 3.5 42.0 - - + -
160B PHE* 4.0 5.2 - - + -
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Residues in contact with ILE 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 ILE* 2.9 21.3 + - + +
122B ASN* 3.2 29.4 - - + +
123B PHE 3.1 0.2 - - - -
124B PHE* 1.3 76.6 - - - +
126B ALA* 1.3 63.0 + - - +
128B TYR* 3.8 2.1 + - - +
129B LEU* 3.5 18.0 + - - +
160B PHE* 3.1 58.0 - - + +
163B LEU* 3.8 12.6 - - + +
164B ARG* 3.3 29.7 - - + +
167B LEU* 3.7 19.3 - - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR* 3.1 23.3 - - - +
107B TYR* 3.7 17.4 - - + -
108B PHE* 4.1 10.1 - - + -
122B ASN 3.8 10.5 - - - +
123B PHE 2.9 4.8 + - - +
125B ILE* 1.3 77.7 - - - +
127B LEU* 1.3 59.6 + - - +
128B TYR 3.2 0.4 - - - -
129B LEU* 3.1 4.4 + - - +
130B ALA* 2.9 28.9 + - - +
167B LEU* 3.6 20.0 - - + -
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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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86B PHE* 3.6 35.7 - - + -
95B ILE 3.8 10.5 - - - +
96B ALA* 4.2 8.3 - - + -
100B LEU* 3.9 28.7 - - + +
101B LEU* 4.0 12.6 - - + -
104B THR* 3.4 6.8 + - - +
123B PHE* 2.9 27.9 + - + +
124B PHE* 3.6 11.4 - - + +
126B ALA* 1.3 77.6 - - - +
128B TYR* 1.3 53.7 + - - +
130B ALA* 3.5 3.0 + - + +
131B ASN* 2.3 55.4 + - - +
144B ILE* 4.4 7.4 - - + -
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE 2.9 16.8 + - - +
125B ILE 3.9 5.8 - - - +
126B ALA 3.2 0.2 - - - -
127B LEU* 1.3 77.7 - - - +
129B LEU* 1.3 57.9 + - - +
131B ASN* 3.5 3.3 - - - +
132B THR* 2.9 27.2 + - - +
141B LYS* 3.3 51.4 + - + +
142B TYR* 3.8 17.8 - - - -
144B ILE* 3.9 12.5 - - + +
145B PHE* 3.5 36.0 - + - -
160B PHE* 4.0 13.0 - + + -
161B LEU* 3.6 16.2 - - + +
164B ARG* 3.3 37.6 + - - -
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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
----------------------------------------------------------
49A ILE* 4.0 28.0 - - + -
107B TYR* 4.0 21.5 - - + -
125B ILE 3.5 11.2 + - - +
126B ALA 3.1 9.3 + - - +
128B TYR* 1.3 77.3 - - - +
130B ALA* 1.3 64.5 + - - +
132B THR* 3.1 11.4 - - + +
133B VAL* 2.9 30.3 + - + +
164B ARG* 4.1 19.0 - - + +
167B LEU* 4.5 13.2 - - + -
168B TRP* 4.2 32.5 - - + +
171B ILE* 4.2 13.7 - - + -
175B ALA* 4.5 3.6 - - + -
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Residues in contact with ALA 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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100B LEU* 4.0 19.7 - - + +
103B MET* 3.9 26.2 - - + +
104B THR 4.9 0.7 - - - +
107B TYR* 3.7 23.7 - - + -
126B ALA 2.9 16.0 + - - +
127B LEU* 3.8 5.2 - - - +
129B LEU* 1.3 74.9 - - - +
131B ASN* 1.3 57.1 + - - +
133B VAL* 3.8 0.7 - - - +
134B GLU* 2.9 34.5 + - - +
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Residues in contact with ASN 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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94B LYS 4.0 2.3 - - - +
95B ILE* 3.0 39.5 + - - +
100B LEU* 3.8 9.8 - - - +
127B LEU* 2.3 50.9 + - - +
128B TYR* 3.5 6.9 - - - +
129B LEU 3.1 0.2 - - - -
130B ALA* 1.3 74.5 - - - +
132B THR* 1.3 60.6 + - - +
135B GLU* 2.9 47.2 + - + +
141B LYS* 3.9 27.4 - - + +
144B ILE* 4.4 4.4 - - - +
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Residues in contact with THR 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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46A SER* 3.2 34.8 + - - +
49A ILE* 4.1 7.6 - - + -
50A ARG* 3.2 25.6 + - - +
128B TYR* 2.9 21.0 + - - +
129B LEU* 3.1 29.6 - - + +
131B ASN* 1.3 74.4 - - - +
133B VAL* 1.3 59.2 + - + +
135B GLU 4.0 2.0 - - - +
141B LYS* 4.0 19.7 - - - +
164B ARG* 3.8 20.2 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.9 22.4 - - + +
50A ARG* 2.9 33.7 + - + +
53A SER* 4.9 2.2 - - - +
150A ARG* 4.3 5.9 + - - +
151A ALA* 5.3 1.7 + - + +
103B MET* 5.0 0.9 - - + -
107B TYR* 4.4 3.8 - - - +
129B LEU* 2.9 21.8 + - + +
130B ALA* 3.8 4.7 - - - +
132B THR* 1.3 78.3 - - - +
134B GLU* 1.3 71.2 + - + +
135B GLU 3.5 0.2 - - - -
175B ALA* 3.5 31.2 - - + +
176B ILE* 3.7 30.1 - - + -
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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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150A ARG* 2.8 35.9 + - - +
151A ALA* 2.9 36.2 - - - +
154A VAL* 3.4 31.0 - - + +
157A ARG* 3.4 27.9 - - - +
100B LEU* 4.3 12.1 - - + -
103B MET* 3.9 17.5 - - + +
130B ALA 2.9 18.3 + - - +
133B VAL* 1.3 86.6 - - - +
135B GLU* 1.3 58.5 + - - +
176B ILE* 4.7 2.3 - - - +
177B VAL 4.9 4.4 + - - +
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Residues in contact with GLU 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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50A ARG* 2.8 18.5 + - - +
157A ARG* 2.5 20.8 + - - -
158A THR* 2.8 37.7 + - + +
94B LYS 4.5 3.1 - - - +
100B LEU* 3.7 4.3 - - + +
131B ASN* 2.9 41.6 + - + +
132B THR* 4.0 4.2 - - - +
134B GLU* 1.3 81.6 - - + +
136B ASP* 1.3 60.9 + - - +
137B GLU* 3.5 14.5 + - + +
138B GLU* 5.4 2.1 - - - +
141B LYS* 5.3 2.9 - - + -
199B ARG* 2.3 33.3 + - - -
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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
------------------------------------------------------------
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