Contacts of the helix formed by residues 114 - 133 (chain B) in PDB entry 6UPQ
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 TYR 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASP* 3.8 26.0 + - - -
113B SER* 1.3 79.3 - - - +
115B LYS* 1.3 96.4 + - + +
116B PRO 3.5 0.2 - - - -
117B ILE* 3.0 16.8 + - + +
118B VAL* 2.9 33.8 + - + +
167B VAL* 4.5 15.7 - - + -
168B THR* 4.1 21.5 + - + +
171B LYS* 3.5 65.0 + - + -
172B LEU* 5.4 0.7 - - + -
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 3.1 47.5 + - + +
114B TYR* 1.3 107.4 - - + +
116B PRO* 1.3 64.7 - - + +
118B VAL* 3.3 4.8 + - - +
119B GLU* 2.8 30.1 + - - +
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Residues in contact with PRO 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.2 40.8 - - + +
79B ARG* 4.7 4.7 - - - -
80B LEU* 3.5 12.4 - - + +
112B ASP 3.6 5.8 - - - +
113B SER* 3.4 14.8 - - - +
115B LYS* 1.3 94.2 - - + +
117B ILE* 1.3 59.3 + - - +
119B GLU* 3.7 17.4 - - + +
120B TYR* 3.2 16.5 + - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.8 34.1 - - + -
47B VAL* 4.2 18.2 - - + -
78B VAL* 4.2 7.4 - - + -
80B LEU* 3.8 10.3 - - + -
101B THR* 3.8 26.0 - - + -
104B PHE* 4.2 6.7 - - + -
113B SER 3.9 17.7 - - - +
114B TYR* 3.0 8.4 + - - +
116B PRO* 1.3 74.4 - - - +
118B VAL* 1.3 64.8 + - - +
120B TYR* 3.2 4.5 + - - +
121B ILE* 3.0 22.7 + - + +
168B THR* 4.2 17.0 - - + -
172B LEU* 4.0 17.0 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 2.9 34.6 + - + +
115B LYS* 3.8 6.3 - - - +
117B ILE* 1.3 73.8 - - - +
119B GLU* 1.3 54.7 + - - +
121B ILE* 3.3 6.6 + - - +
122B ASP* 2.7 53.3 + - - +
171B LYS* 3.9 14.8 - - + +
172B LEU* 3.7 21.1 - - + -
175B LYS* 4.1 16.4 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS 2.8 17.7 + - - +
116B PRO* 3.7 15.6 - - + +
117B ILE 3.2 0.2 - - - -
118B VAL* 1.3 78.0 - - - +
120B TYR* 1.3 57.1 + - - +
122B ASP* 3.5 5.3 + - - +
123B ALA* 2.9 31.2 + - + +
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Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.7 1.6 - - + -
80B LEU* 3.3 36.1 - - + -
82B ALA* 3.9 15.6 - - + +
97B THR* 4.7 4.9 - - - +
99B VAL* 3.6 31.9 - - + +
116B PRO 3.2 7.4 + - - +
117B ILE 3.2 2.0 + - - +
119B GLU* 1.3 75.4 - - - +
121B ILE* 1.3 70.3 + - + +
123B ALA* 3.1 12.3 + - - -
124B GLN* 3.1 57.7 + - + +
145B THR* 4.7 5.4 + - - -
147B ILE* 3.9 25.4 - - + -
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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
----------------------------------------------------------
45B LEU* 3.9 20.9 - - + -
117B ILE* 3.0 18.5 + - + +
118B VAL* 3.7 5.2 - - - +
120B TYR* 1.3 78.7 - - + +
122B ASP* 1.3 63.6 + - - +
124B GLN* 3.3 7.7 + - - +
125B PHE* 3.2 44.7 + - + -
147B ILE* 4.1 26.1 + - + +
172B LEU* 3.7 28.9 - - + -
175B LYS* 3.8 23.1 - - + +
176B VAL* 4.5 12.6 - - + -
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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
----------------------------------------------------------
118B VAL* 2.7 32.5 + - - +
119B GLU* 3.9 5.3 - - - +
121B ILE* 1.3 72.8 - - - +
123B ALA* 1.3 57.9 + - - +
125B PHE* 3.2 15.5 + - - +
126B GLU* 2.9 29.8 + - - +
175B LYS* 2.6 42.9 + - - +
297B TYR* 3.9 16.3 + - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 2.9 21.4 + - + +
120B TYR* 3.1 7.8 + - - +
122B ASP* 1.3 76.0 - - - +
124B GLN* 1.3 68.8 + - - +
126B GLU* 3.4 5.8 + - - +
127B ALA* 2.9 28.1 + - - +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.1 59.8 + - + +
121B ILE* 3.8 6.5 - - - +
123B ALA* 1.3 85.6 - - - +
125B PHE* 1.3 65.4 + - - +
127B ALA* 3.8 5.5 - - - +
128B TYR* 3.1 23.2 + - - +
142B TYR* 4.8 0.3 + - - -
145B THR* 2.6 57.1 + - - +
146B ARG* 3.6 17.6 - - - +
147B ILE 4.9 1.6 - - - +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.2 29.3 + - + -
122B ASP* 3.4 15.3 - - - +
124B GLN* 1.3 76.8 - - - +
126B GLU* 1.3 56.3 + - - +
128B TYR 3.2 1.7 + - - -
129B LEU* 2.9 24.9 + - - +
146B ARG* 3.8 22.0 - - + -
147B ILE 5.7 2.5 - - - -
175B LYS* 3.3 36.1 - - + -
289B THR* 4.5 6.5 - - + -
293B HIS* 3.8 11.2 - - + -
294B TYR* 3.5 53.0 - + + -
297B TYR* 3.6 41.3 - + + -
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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
----------------------------------------------------------
122B ASP 2.9 13.6 + - - +
123B ALA* 3.8 7.2 - - - +
125B PHE* 1.3 73.0 - - - +
127B ALA* 1.3 61.2 + - - +
129B LEU* 3.2 13.0 + - - +
130B GLN* 2.8 65.4 + - + +
297B TYR* 2.4 43.0 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA 2.9 17.6 + - - +
124B GLN* 3.8 9.4 - - - +
126B GLU* 1.3 77.1 - - - +
128B TYR* 1.3 61.3 + - - +
130B GLN* 3.4 7.4 + - - +
131B GLU* 3.1 23.7 + - - +
142B TYR* 3.5 18.7 + - - +
145B THR* 4.7 3.4 - - - +
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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
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124B GLN 3.1 14.2 + - - +
125B PHE 3.2 7.8 + - - +
127B ALA* 1.3 76.5 - - - +
129B LEU* 1.3 62.0 + - - +
131B GLU* 3.1 5.7 + - - +
132B GLU* 3.0 42.2 + - + +
139B LEU* 4.4 19.0 + - + +
142B TYR* 3.5 36.0 + + + -
144B ASP* 3.8 10.3 - - + -
146B ARG* 3.4 50.4 + - + -
290B HIS* 4.0 12.8 - + - -
294B TYR* 3.6 17.9 - + + -
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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
----------------------------------------------------------
125B PHE 2.9 16.0 + - - +
126B GLU* 3.6 26.2 - - - +
128B TYR* 1.3 76.8 - - - +
130B GLN* 1.3 64.5 + - - +
132B GLU* 3.0 18.7 + - + +
133B LEU* 3.0 38.5 + - + +
294B TYR* 3.2 23.5 + - + +
297B TYR* 4.4 11.4 - - + -
298B ARG* 4.1 24.0 - - + +
300B CYS 5.3 6.5 - - - +
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Residues in contact with GLN 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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126B GLU* 2.8 49.3 + - + +
127B ALA* 3.8 7.6 - - - +
129B LEU* 1.3 77.0 - - - +
131B GLU* 1.3 62.0 + - - +
133B LEU* 3.3 29.7 + - - +
134B LYS* 3.4 21.2 + - - +
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Residues in contact with GLU 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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127B ALA 3.1 13.0 + - - +
128B TYR* 3.1 12.0 + - - +
130B GLN* 1.3 78.1 - - - +
132B GLU* 1.3 61.8 + - - +
134B LYS* 2.9 55.9 + - - +
137B ARG* 3.8 10.4 - - - +
138B SER* 4.8 12.5 + - - +
139B LEU* 3.9 18.5 - - + +
142B TYR* 3.5 46.5 - - + +
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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
----------------------------------------------------------
128B TYR* 3.0 34.8 + - + +
129B LEU* 3.0 14.1 + - + +
131B GLU* 1.3 75.5 - - - +
133B LEU* 1.3 64.3 + - + +
134B LYS 3.6 1.7 + - - +
137B ARG* 2.8 32.7 + - - +
139B LEU* 4.1 17.7 - - + +
290B HIS* 4.2 7.4 - - - -
294B TYR* 2.4 35.1 + - - -
295B GLU* 5.5 0.2 - - - +
298B ARG* 3.8 14.5 + - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.0 42.8 + - + +
130B GLN* 3.3 23.1 + - - +
131B GLU 3.2 0.6 - - - -
132B GLU* 1.3 77.4 - - + +
134B LYS* 1.3 65.9 + - - +
135B ILE* 3.7 5.2 + - - +
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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