Contacts of the helix formed by residues 120 - 134 (chain Y) in PDB entry 3UBT
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 120 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D T 3.4 28.1 + - - +
78Y GLY* 5.1 2.8 - - - +
114Y MET* 4.5 11.6 + - - +
115Y MET* 4.4 4.7 - - - +
117Y GLN* 3.0 24.2 - - + +
118Y ARG 2.9 2.2 - - - -
119Y HIS* 1.3 79.8 - - - +
121Y LYS* 1.3 67.6 + - - +
122Y ALA* 3.3 31.5 + - - +
123Y VAL* 3.2 11.1 + - + +
124Y GLN* 3.0 24.6 + - - +
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Residues in contact with LYS 121 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Y GLY 3.7 11.7 - - - +
79Y SER* 3.3 24.7 - - - +
119Y HIS 4.2 1.0 + - - -
120Y ASN* 1.3 75.1 + - - +
122Y ALA* 1.3 65.3 + - - +
124Y GLN* 3.2 8.8 + - - +
125Y GLU* 3.1 46.3 + - + +
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Residues in contact with ALA 122 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Y SER* 4.7 1.3 - - - -
78Y GLY* 3.8 21.7 + - - +
79Y SER* 4.4 3.1 - - - +
80Y LEU 4.8 0.4 - - - +
115Y MET* 4.0 23.6 - - + -
120Y ASN* 3.3 12.1 + - - +
121Y LYS* 1.3 79.3 - - - +
123Y VAL* 1.3 62.1 + - - +
125Y GLU* 3.2 14.7 + - - +
126Y PHE* 3.0 39.0 + - + -
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Residues in contact with VAL 123 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115Y MET* 3.6 35.9 - - - +
117Y GLN 3.1 29.2 - - - +
118Y ARG* 3.9 11.4 - - - -
120Y ASN* 3.2 14.7 + - + +
122Y ALA* 1.3 75.8 - - - +
124Y GLN* 1.3 58.5 + - - +
126Y PHE* 3.1 10.2 + - - +
127Y ILE* 2.9 31.8 + - + +
139Y ILE* 3.7 30.1 - - + -
158Y TYR* 3.8 5.6 - - - +
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Residues in contact with GLN 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Y ARG* 2.8 38.9 + - - +
119Y HIS* 5.1 1.3 - - - +
120Y ASN 3.0 11.9 + - - +
121Y LYS* 3.2 10.3 + - - +
123Y VAL* 1.3 76.7 - - - +
125Y GLU* 1.3 62.5 + - + +
127Y ILE* 3.6 19.3 + - - +
128Y GLN* 3.2 22.7 + - - +
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Residues in contact with GLU 125 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y SER* 3.6 9.5 - - - -
80Y LEU* 3.0 52.3 + - + +
121Y LYS* 3.1 36.0 + - + +
122Y ALA* 3.4 12.8 - - - +
124Y GLN* 1.3 74.6 - - + +
126Y PHE* 1.3 65.5 + - - +
128Y GLN* 3.3 10.3 + - - +
129Y GLU* 3.2 28.0 + - - +
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Residues in contact with PHE 126 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Y TRP* 3.7 58.3 - + + -
75Y SER* 4.0 18.4 - - - -
80Y LEU* 3.9 19.5 - - + -
91Y PHE* 4.4 6.7 - + - -
115Y MET* 3.9 26.7 - - + -
122Y ALA* 3.0 20.7 + - + -
123Y VAL* 3.3 7.6 - - - +
125Y GLU* 1.3 76.3 - - - +
127Y ILE* 1.3 63.7 + - - +
129Y GLU* 3.0 9.0 + - - +
130Y PHE* 3.0 41.9 + - + -
158Y TYR* 3.5 25.1 - - + -
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Residues in contact with ILE 127 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Y ARG* 3.4 39.9 - - + +
123Y VAL* 2.9 36.1 + - + +
124Y GLN* 3.8 25.6 - - - +
125Y GLU 3.3 0.2 - - - -
126Y PHE* 1.3 76.2 - - + +
128Y GLN* 1.3 57.9 + - - +
130Y PHE* 3.4 9.2 + - - +
131Y ASP* 2.9 32.0 + - + +
135Y TYR 5.1 0.3 - - - +
137Y VAL* 5.0 14.3 - - + +
139Y ILE* 4.3 9.2 - - + -
158Y TYR* 5.2 0.7 - - + -
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Residues in contact with GLN 128 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Y GLN 3.2 15.1 + - - +
125Y GLU* 3.7 9.8 - - - +
126Y PHE 3.2 0.2 - - - -
127Y ILE* 1.3 76.8 - - - +
129Y GLU* 1.3 70.0 + - + +
131Y ASP* 3.6 7.3 - - + +
132Y ASN* 2.9 30.0 + - + +
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Residues in contact with GLU 129 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y LEU* 3.9 26.1 - - + +
91Y PHE* 4.3 22.1 - - + -
92Y TYR* 4.1 19.1 + - - -
95Y ILE* 4.4 17.3 - - + +
125Y GLU 3.2 15.8 + - - +
126Y PHE 3.0 7.0 + - - +
128Y GLN* 1.3 84.8 - - - +
130Y PHE* 1.3 59.6 + - + +
132Y ASN* 3.3 16.1 + - - +
133Y ALA* 2.9 26.0 + - - +
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Residues in contact with PHE 130 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Y TRP* 4.7 13.0 - + - -
91Y PHE* 4.6 16.6 - + - -
94Y TYR* 4.4 11.0 - + - -
95Y ILE* 3.9 24.5 - - + -
98Y LEU* 4.3 11.9 - - + -
106Y PHE* 3.7 29.4 - + + -
108Y ALA* 5.5 0.7 - - + -
126Y PHE* 3.0 34.0 + - + +
127Y ILE* 3.8 3.4 - - - +
129Y GLU* 1.3 72.2 - - - +
131Y ASP* 1.3 61.1 + - - +
133Y ALA* 3.0 6.9 + - - +
134Y GLY 3.0 21.7 + - - -
135Y TYR* 3.0 13.1 + - + +
137Y VAL* 3.5 33.2 - - + -
158Y TYR* 3.9 25.4 - + + -
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Residues in contact with ASP 131 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Y ILE* 2.9 23.0 + - + +
128Y GLN* 3.6 7.2 - - - +
129Y GLU 3.3 0.2 - - - -
130Y PHE* 1.3 75.6 - - - +
132Y ASN* 1.3 61.2 + - - +
134Y GLY* 2.8 15.4 + - - -
135Y TYR 3.5 13.5 + - - +
136Y ASP* 4.6 4.2 - - - +
163Y LYS* 3.1 45.1 + - - +
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Residues in contact with ASN 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Y ILE* 5.8 1.6 - - - +
99Y LYS* 3.1 31.1 + - - +
128Y GLN* 2.9 19.5 + - + +
129Y GLU* 3.4 17.3 + - - +
131Y ASP* 1.3 78.7 + - - +
133Y ALA* 1.3 61.1 + - - +
134Y GLY* 3.2 1.2 + - - -
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Residues in contact with ALA 133 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Y ILE* 4.6 7.9 - - + -
98Y LEU* 4.5 14.6 - - + -
99Y LYS* 3.6 34.3 - - + +
129Y GLU 2.9 13.9 + - - +
130Y PHE* 3.0 15.2 + - - +
132Y ASN* 1.3 76.6 - - - +
134Y GLY* 1.3 57.0 + - - +
135Y TYR* 3.5 24.4 - - + -
162Y ARG* 4.9 4.9 + - - -
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Residues in contact with GLY 134 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Y ASP 2.8 13.7 + - - -
132Y ASN 3.0 1.3 - - - -
133Y ALA* 1.3 78.4 - - - +
135Y TYR* 1.3 72.5 + - - +
162Y ARG* 3.5 14.3 + - - +
163Y LYS* 3.4 34.7 + - - +
164Y GLU* 4.9 0.9 - - - +
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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
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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