Contacts of the helix formed by residues 128 - 141 (chain H) in PDB entry 2VUT
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 TRP 128 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113H MET* 3.6 38.3 - - + +
114H PRO* 3.4 15.0 - - + +
116H HIS* 3.7 21.5 - + - -
125H VAL* 2.8 30.2 + - + +
126H PRO 3.2 0.4 - - - -
127H MET* 1.3 88.5 - - - +
129H ALA* 1.3 54.6 + - - +
130H PRO* 3.1 2.5 - - - -
131H LYS* 2.8 38.0 + - - +
181H PHE* 6.3 0.7 - + - -
261H GLN* 3.3 20.7 - - - +
265H ILE* 4.6 10.1 - - + -
269H PHE* 3.4 34.5 - + - -
276H TYR* 3.4 41.7 - + - -
1354H NAD 3.6 20.3 + + - -
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Residues in contact with ALA 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H PRO 3.3 10.6 + - - -
115H ASP* 3.6 33.8 - - + +
124H ALA* 3.8 16.6 - - + -
125H VAL 3.0 10.1 + - - +
126H PRO* 5.3 0.7 - - + -
128H TRP* 1.3 75.9 - - - +
130H PRO* 1.3 69.2 - - + +
132H PHE* 3.0 19.3 + - - +
133H THR* 3.7 5.7 + - - -
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Residues in contact with PRO 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H ASP* 6.0 0.2 - - - +
88H GLU* 4.3 21.5 - - + +
89H ILE* 3.7 28.1 - - + +
126H PRO* 3.0 28.5 - - + +
127H MET* 4.1 2.2 - - - -
128H TRP 3.1 7.2 - - - +
129H ALA* 1.3 93.6 - - + +
131H LYS* 1.3 61.5 + - - +
133H THR* 3.0 17.4 + - - +
134H VAL* 3.3 14.0 + - - +
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Residues in contact with LYS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ASN* 3.8 8.8 + - - -
81H THR* 3.0 13.5 + - - +
88H GLU* 2.7 33.8 + - - +
110H TYR* 3.3 26.4 - - + +
111H SER 3.6 15.4 + - - +
112H SER* 4.0 2.0 - - - -
113H MET* 3.6 37.2 - - + +
127H MET 3.6 15.0 - - - +
128H TRP 2.8 16.2 + - - +
130H PRO* 1.3 72.2 - - - +
132H PHE* 1.3 57.7 + - - +
134H VAL* 3.0 5.9 + - - +
135H GLU* 2.9 24.8 + - - +
1354H NAD 3.0 32.2 + - - -
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H SER* 4.0 3.1 - - - -
113H MET 3.7 16.9 + - - +
114H PRO* 5.3 3.6 - - + -
115H ASP* 4.5 9.6 - - + +
118H LEU* 3.7 28.3 - - + -
119H TYR* 4.1 19.7 - - - -
129H ALA 3.0 12.9 + - - +
131H LYS* 1.3 78.8 - - - +
133H THR* 1.3 64.2 + - - +
135H GLU* 3.3 6.6 + - - +
136H ASN* 3.1 50.9 + - - -
149H TYR* 4.0 16.8 - - - -
215H ARG* 3.6 26.7 - - - -
279H LEU* 5.1 0.9 - - + -
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Residues in contact with THR 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 3.9 36.2 - - + +
93H LYS* 4.3 12.1 - - - +
129H ALA 3.7 4.6 + - - -
130H PRO 3.0 11.2 + - - -
132H PHE* 1.3 81.5 - - - +
134H VAL* 1.3 59.2 + - - +
136H ASN* 3.4 9.8 + - + +
137H TYR* 3.0 24.6 + - - +
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Residues in contact with VAL 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H GLU 3.8 21.1 - - - +
89H ILE* 4.0 11.4 - - + +
92H GLY* 3.4 34.3 - - - +
93H LYS* 5.0 2.2 - - - -
110H TYR* 3.3 40.6 - - + +
130H PRO 3.5 13.9 - - - +
131H LYS* 3.0 1.7 + - - +
133H THR* 1.3 74.9 - - - +
135H GLU* 1.3 59.5 + - - +
137H TYR* 3.0 7.3 + - + +
138H VAL* 2.8 38.5 + - + +
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Residues in contact with GLU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H TYR* 4.2 2.6 - - - -
112H SER* 2.9 17.8 + - - +
131H LYS 2.9 12.2 + - - +
132H PHE* 3.3 13.5 + - - +
134H VAL* 1.3 76.9 - - - +
136H ASN* 1.3 64.8 + - - +
138H VAL* 2.9 15.0 + - - +
139H ARG* 2.7 46.2 + - - +
147H PHE* 3.3 39.7 - - + -
149H TYR* 2.6 25.6 + - - -
215H ARG* 2.8 22.7 + - - +
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Residues in contact with ASN 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PHE* 3.1 48.0 + - - +
133H THR* 3.6 9.7 - - - +
135H GLU* 1.3 77.2 - - - +
137H TYR* 1.3 56.7 + - - +
139H ARG* 3.6 19.9 + - - +
140H GLN* 3.0 30.5 + - - +
215H ARG* 4.8 2.6 - - - +
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Residues in contact with TYR 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H LYS* 3.7 54.7 - - + -
96H ALA* 3.7 14.1 - - + -
97H ASP* 2.8 33.3 + - - -
133H THR 3.0 14.5 + - - +
134H VAL* 3.0 12.5 + - + +
136H ASN* 1.3 76.3 - - - +
138H VAL* 1.3 64.4 + - - +
140H GLN* 3.3 32.3 + - - +
141H LEU* 3.1 42.6 + - + +
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H ALA* 4.6 14.4 - - + -
108H TYR* 3.9 31.2 - - + +
110H TYR* 4.5 3.6 - - + -
134H VAL* 2.8 32.4 + - + +
135H GLU* 2.9 6.3 + - - +
137H TYR* 1.3 75.7 - - - +
139H ARG* 1.3 63.0 + - - +
141H LEU* 3.0 16.1 + - - +
142H GLY 3.4 6.1 + - - -
143H LEU* 3.7 15.4 + - + +
145H SER* 3.4 32.1 - - - +
147H PHE* 3.7 13.9 - - + -
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Residues in contact with ARG 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H GLU* 2.7 49.0 + - - +
136H ASN* 3.8 17.2 - - - +
138H VAL* 1.3 77.6 - - - +
140H GLN* 1.3 58.0 + - - +
142H GLY* 2.9 21.9 + - - +
143H LEU 5.3 1.8 - - - +
145H SER* 4.8 4.5 - - - +
147H PHE* 3.4 26.7 - - + -
213H GLY* 3.7 30.9 + - - -
215H ARG* 3.5 26.7 - - - +
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Residues in contact with GLN 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H ASN 3.0 20.6 + - - +
137H TYR* 3.4 35.8 - - - +
138H VAL 3.2 0.4 - - - -
139H ARG* 1.3 77.4 - - - +
141H LEU* 1.3 65.4 + - + +
142H GLY* 3.1 1.6 + - - -
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H ALA* 3.5 30.3 - - + +
97H ASP* 3.5 24.0 - - - +
100H LYS* 3.2 46.3 + - + +
137H TYR* 3.1 41.5 + - + +
138H VAL 3.0 10.0 + - - +
140H GLN* 1.3 84.7 - - - +
142H GLY* 1.3 60.6 + - - +
143H LEU* 3.5 11.4 + - + +
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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