Contacts of the helix formed by residues 111 - 127 (chain B) in PDB entry 4UTX
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 ASN 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PRO 5.2 0.4 - - - -
112A PRO* 6.0 4.0 - - + -
57B VAL* 2.8 24.5 + - - +
60B GLU* 3.4 31.5 - - + +
61B SER* 2.7 25.0 + - - +
109B MET 4.9 0.2 - - - +
110B PRO* 1.3 76.0 - - - +
112B PRO* 1.3 75.8 - - + +
113B ALA* 2.9 28.1 + - - +
114B HIS* 3.2 20.8 + - - +
115B LEU* 3.4 14.9 + - - +
290B GLY* 4.6 0.3 - - - -
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Residues in contact with PRO 112 (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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109A MET* 3.5 33.6 - - + +
110A PRO 4.5 8.1 - - - +
111A ASN* 5.7 3.6 - - - -
112A PRO* 6.0 3.6 - - + -
111B ASN* 1.3 91.2 - - + +
113B ALA* 1.3 58.9 + - - +
115B LEU* 3.3 2.4 + - + -
116B ALA* 2.9 30.5 + - - +
290B GLY* 3.5 27.6 - - - +
294B PRO* 4.0 2.9 - - + +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 4.2 10.3 - - + -
111B ASN* 2.9 12.6 + - - +
112B PRO* 1.3 74.9 - - - +
114B HIS* 1.3 66.5 + - - +
115B LEU 3.0 2.0 + - - -
116B ALA* 3.3 3.3 + - - +
117B ILE* 3.1 30.6 + - + +
244B VAL* 5.3 0.2 - - + -
289B CYS* 3.8 38.8 - - + -
290B GLY* 4.0 2.2 - - - -
293B LEU* 3.9 16.2 - - + -
294B PRO* 4.9 0.4 - - - -
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 3.4 38.9 - - + +
58B SER* 4.5 4.4 + - - -
61B SER* 3.5 7.9 - - - -
110B PRO* 3.7 17.4 - - + +
111B ASN* 3.2 36.1 + - - +
113B ALA* 1.3 77.8 - - - +
115B LEU* 1.3 61.2 + - - +
117B ILE* 3.6 7.3 - - - +
118B ALA* 3.2 15.4 + - - +
137B ASN* 5.8 0.6 + - - -
139B ASP* 4.9 0.4 + - - -
141B LEU* 3.5 35.7 - - + +
142B HIS* 3.6 35.6 + + - +
145B ALA* 3.6 15.2 - - + +
147B SER* 4.5 1.7 + - - -
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Residues in contact with LEU 115 (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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109A MET* 3.4 16.4 - - + -
110A PRO* 3.7 35.0 - - + +
115A LEU* 3.8 24.9 - - + -
144A ARG 4.3 11.4 - - - +
110B PRO* 4.3 2.7 - - + +
111B ASN 3.4 18.5 + - - +
112B PRO* 3.3 6.0 + - + +
113B ALA 3.0 0.6 - - - -
114B HIS* 1.3 73.9 - - - +
116B ALA* 1.3 62.2 + - - +
117B ILE 3.0 1.6 - - - -
118B ALA* 2.7 22.5 + - - +
119B GLU* 2.8 23.4 + - + +
145B ALA* 3.9 28.3 - - + +
1301B DMS 4.3 12.8 - - + -
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Residues in contact with ALA 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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109A MET* 3.3 14.3 - - + +
112B PRO 2.9 18.2 + - - +
113B ALA* 3.3 5.1 + - - +
115B LEU* 1.3 75.5 - - - +
117B ILE* 1.3 58.1 + - - +
119B GLU* 3.5 1.8 + - - +
120B CYS* 2.9 30.0 + - - +
123B ARG* 5.2 1.0 + - - -
293B LEU* 4.8 1.3 - - + -
294B PRO* 3.8 33.7 - - + +
297B LEU* 4.0 16.8 - - + +
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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
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51B ILE* 4.1 31.0 - - + -
53B THR* 4.6 3.6 - - + -
57B VAL* 5.8 1.8 - - + -
113B ALA* 3.1 17.6 + - + +
114B HIS 3.6 6.1 - - - +
116B ALA* 1.3 77.4 - - - +
118B ALA* 1.3 58.1 + - - +
120B CYS* 2.8 23.3 + - - +
121B GLU* 2.8 14.7 + - - +
131B VAL* 5.0 0.9 - - + -
133B ILE* 3.8 32.1 - - + -
142B HIS* 4.1 22.9 - - + +
147B SER* 3.8 8.5 - - - +
244B VAL* 5.2 3.6 - - + -
293B LEU* 3.9 22.0 - - + -
297B LEU* 4.2 8.3 - - + -
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Residues in contact with ALA 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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114B HIS 3.2 9.0 + - - +
115B LEU* 2.7 13.3 + - - +
117B ILE* 1.3 75.9 - - - +
119B GLU* 1.3 63.2 + - + +
121B GLU* 3.6 3.9 + - - +
122B ALA* 3.2 21.3 + - - +
145B ALA* 3.2 28.3 - - + +
146B GLY 3.7 17.2 - - - +
147B SER* 3.3 22.0 - - - +
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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
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106A ARG 5.7 0.2 - - - +
109A MET* 3.4 16.7 - - + +
110A PRO* 4.7 0.7 - - - +
144A ARG* 2.9 62.0 + - - +
115B LEU* 2.8 28.5 + - + +
116B ALA* 4.1 2.9 - - - +
118B ALA* 1.3 72.7 - - + +
120B CYS* 1.3 61.3 + - - +
122B ALA* 3.2 7.2 + - - +
123B ARG* 2.8 42.9 + - - +
145B ALA 5.8 0.4 - - - +
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Residues in contact with CYS 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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43B PHE* 4.0 32.3 - - - -
49B ILE* 5.5 1.6 - - - -
51B ILE* 5.9 2.2 - - + -
116B ALA 2.9 15.3 + - - +
117B ILE* 2.8 14.4 + - - +
119B GLU* 1.3 76.0 - - - +
121B GLU* 1.3 54.2 + - - +
123B ARG* 3.1 20.2 + - - +
124B LEU* 2.8 51.2 + - - +
131B VAL* 4.5 10.3 - - + -
297B LEU* 4.3 14.6 - - + -
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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
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117B ILE 2.8 12.3 + - - +
118B ALA 3.8 3.8 - - - +
120B CYS* 1.3 74.9 - - - +
122B ALA* 1.3 54.3 - - - +
124B LEU* 3.7 1.2 - - - +
125B GLY* 2.8 33.1 + - - -
129B ARG 5.0 0.7 - - - +
131B VAL* 3.7 41.6 + - + +
133B ILE* 3.6 7.6 - - - +
146B GLY 5.0 0.4 - - - -
147B SER* 3.2 26.9 + - - -
148B LYS* 2.9 24.8 + - + +
149B HIS* 2.9 41.7 + - + +
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Residues in contact with ALA 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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118B ALA 3.2 11.0 + - - +
119B GLU* 3.2 12.1 + - - +
120B CYS 3.1 0.4 - - - -
121B GLU* 1.3 78.3 - - - +
123B ARG* 1.3 66.4 + - - +
125B GLY* 3.0 11.7 + - - -
126B GLN* 3.3 17.1 + - - +
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Residues in contact with ARG 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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106A ARG* 5.3 12.9 + - - +
43B PHE* 4.5 3.6 - - - -
116B ALA 5.2 0.8 + - - -
119B GLU* 2.8 36.4 + - - +
120B CYS* 3.6 19.3 - - - +
122B ALA* 1.3 73.3 - - - +
124B LEU* 1.3 70.1 + - + +
126B GLN* 3.3 22.2 + - - +
127B GLN* 3.5 28.3 + - - +
297B LEU* 2.6 32.7 + - - +
298B GLU* 3.9 15.9 + - - +
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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
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43B PHE* 4.5 7.4 - - + -
46B ALA 5.0 0.4 - - - +
49B ILE* 4.1 17.9 - - + -
120B CYS* 2.8 35.0 + - - +
121B GLU 4.0 2.2 - - - +
123B ARG* 1.3 89.8 - - + +
125B GLY* 1.3 60.5 + - - +
127B GLN* 3.0 20.6 + - - +
129B ARG* 2.9 78.9 + - + +
131B VAL* 3.9 24.9 - - + -
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Residues in contact with GLY 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 GLU 2.8 17.1 + - - -
122B ALA* 3.0 5.3 + - - -
124B LEU* 1.3 76.2 - - - +
126B GLN* 1.3 55.4 + - - +
128B GLY* 2.9 20.1 + - - -
129B ARG 3.5 11.6 + - - -
149B HIS* 6.4 2.7 - - - -
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Residues in contact with GLN 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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122B ALA 3.3 9.6 + - - +
123B ARG* 3.6 19.7 - - - +
124B LEU 3.3 0.2 - - - -
125B GLY* 1.3 76.5 - - - +
127B GLN* 1.3 59.5 + - + +
128B GLY 3.1 3.4 + - - -
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Residues in contact with GLN 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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123B ARG* 3.5 35.1 + - - +
124B LEU* 3.0 14.8 + - - +
126B GLN* 1.3 77.6 - - + +
128B GLY* 1.3 61.3 + - - +
129B ARG* 2.9 41.8 + - - +
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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