Contacts of the helix formed by residues 128 - 141 (chain E) in PDB entry 2VUU
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E MET* 3.1 41.0 - - + +
114E PRO* 3.4 13.6 - - + +
116E HIS* 3.9 17.7 - + - -
125E VAL* 2.8 30.4 + - + +
126E PRO 3.3 0.6 - - - -
127E MET* 1.3 88.1 - - - +
129E ALA* 1.3 67.3 + - - +
130E PRO* 3.3 2.0 - - - -
131E LYS* 3.1 23.7 + - - +
181E PHE* 6.5 0.4 - + - -
261E GLN* 3.8 13.2 - - - +
265E ILE* 4.0 13.7 - - + -
269E PHE* 3.4 35.2 - + - -
276E TYR* 3.5 40.4 + + - -
1353E NAP 3.8 19.4 + + - -
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E PRO 3.0 11.7 + - - +
115E ASP* 3.3 40.8 - - - +
124E ALA* 3.8 14.6 - - + -
125E VAL 2.9 13.4 + - - +
126E PRO* 5.6 0.2 - - + -
128E TRP* 1.3 75.2 - - - +
130E PRO* 1.4 69.4 - - + +
132E PHE* 2.9 21.5 + - - +
133E THR* 3.7 5.3 + - - -
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Residues in contact with PRO 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E GLU* 4.8 16.8 - - + +
89E ILE* 3.6 27.9 - - + +
126E PRO* 3.2 30.1 - - + +
127E MET* 4.3 1.6 - - - -
128E TRP 3.3 4.9 - - - +
129E ALA* 1.4 93.7 - - + +
131E LYS* 1.3 61.5 - - + +
133E THR* 3.1 26.1 - - - +
134E VAL* 3.5 4.6 + - - +
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Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ASN* 3.6 14.1 + - - -
81E THR* 3.1 19.4 + - - +
88E GLU* 3.6 18.0 + - + +
110E TYR* 3.4 26.6 - - - +
111E SER* 4.2 7.9 + - - +
112E SER* 3.6 6.8 + - - +
113E MET* 3.7 37.2 - - + +
127E MET 3.4 17.0 - - - +
128E TRP 3.1 9.6 + - - +
129E ALA 3.0 0.2 + - - -
130E PRO* 1.3 74.4 - - + +
132E PHE* 1.3 60.1 + - - +
134E VAL* 2.9 7.4 + - - +
135E GLU 2.8 24.3 + - - -
1353E NAP 2.7 36.1 + - - -
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Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E SER* 3.6 7.7 + - - -
113E MET 3.5 14.2 + - - +
114E PRO* 5.7 1.1 - - + -
115E ASP* 4.4 16.4 - - + -
118E LEU* 4.1 26.2 - - + -
119E TYR* 4.4 16.6 - - - -
129E ALA 2.9 12.5 + - - +
131E LYS* 1.3 78.3 - - - +
133E THR* 1.3 64.5 + - - +
135E GLU* 3.2 34.6 - - - +
136E ASN* 3.2 36.3 + - - +
149E TYR* 4.1 5.8 - - - -
215E ARG* 3.9 25.6 - - - -
279E LEU* 6.1 0.7 - - + -
139F ARG 3.7 16.4 - - - -
140F GLN 4.5 3.6 - - - -
142F GLY* 4.9 3.8 - - - -
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Residues in contact with THR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ILE* 4.0 27.7 - - + +
93E LYS* 5.2 7.6 - - - +
115E ASP* 5.1 4.2 + - - -
129E ALA 3.8 6.9 + - - -
130E PRO* 3.1 17.6 + - - +
132E PHE* 1.3 80.6 - - - +
134E VAL* 1.3 64.1 + - - +
136E ASN* 3.3 9.0 + - - +
137E TYR* 3.2 19.6 + - - +
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E GLU 3.6 24.5 - - - +
89E ILE* 3.8 19.7 - - + +
92E GLY* 3.6 27.6 - - - +
93E LYS* 5.2 2.2 - - + -
108E TYR* 6.0 0.2 - - - +
110E TYR* 3.5 35.2 - - + +
130E PRO 3.5 8.5 + - - +
131E LYS* 2.9 8.8 + - - +
133E THR* 1.3 73.4 - - - +
135E GLU* 1.3 66.7 + - - +
137E TYR* 3.0 9.1 + - + +
138E VAL* 2.9 27.6 + - + +
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 4.0 2.4 - - - -
112E SER* 2.9 15.2 + - - +
131E LYS 2.8 11.8 + - - +
132E PHE* 3.2 22.5 - - - +
134E VAL* 1.3 76.9 - - - +
136E ASN* 1.3 61.6 + - - +
138E VAL 3.2 2.1 + - - -
139E ARG* 3.0 39.2 + - - +
147E PHE* 3.4 42.8 - - + -
149E TYR* 2.6 23.6 + - - -
215E ARG* 2.8 30.4 + - - +
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Residues in contact with ASN 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 3.2 43.4 + - - +
133E THR* 3.7 9.5 - - - +
134E VAL 3.3 0.2 - - - -
135E GLU* 1.3 78.9 - - - +
137E TYR* 1.3 58.7 + - - +
139E ARG* 3.4 23.6 + - - +
140E GLN* 2.9 27.6 + - - +
215E ARG* 5.0 2.8 - - - +
136F ASN* 4.0 16.1 - - - +
139F ARG* 3.4 35.9 - - - +
140F GLN* 4.0 5.7 + - + +
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Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLY 5.1 0.4 - - - -
93E LYS* 3.7 54.3 - - + -
96E ALA* 4.0 9.9 - - + -
97E ASP* 2.8 24.7 + - - -
133E THR 3.2 12.2 + - - +
134E VAL* 3.0 13.5 + - - +
136E ASN* 1.3 75.2 - - - +
138E VAL* 1.3 65.1 + - - +
140E GLN* 3.0 34.9 - - - +
141E LEU* 3.0 53.8 + - + +
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA* 4.0 16.2 - - + -
108E TYR* 3.9 24.7 - - + -
110E TYR* 4.9 1.6 - - + -
134E VAL* 2.9 28.1 + - + +
135E GLU* 3.5 8.3 - - - +
137E TYR* 1.3 78.9 - - + +
139E ARG* 1.3 61.6 + - - +
141E LEU* 3.2 12.5 + - - +
142E GLY 3.3 7.4 + - - -
143E LEU* 3.4 28.2 + - + -
145E SER* 3.5 29.4 - - - +
147E PHE* 3.7 13.0 - - + -
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Residues in contact with ARG 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU* 3.0 46.5 + - - +
136E ASN* 3.5 24.8 - - - +
137E TYR 3.3 0.2 - - - -
138E VAL* 1.3 77.0 - - - +
140E GLN* 1.3 59.6 + - - +
142E GLY* 3.2 10.0 + - - +
143E LEU 5.3 1.1 - - - +
145E SER* 4.9 4.5 - - - +
147E PHE* 3.5 26.0 - - + -
213E GLY* 3.5 27.0 + - - -
215E ARG* 3.4 23.4 - - - +
132F PHE* 4.4 0.2 - - - -
139F ARG* 3.6 22.0 - - - +
212F ASN 5.6 0.4 + - - -
213F GLY* 3.4 24.0 + - - -
215F ARG* 2.8 42.1 + - - +
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Residues in contact with GLN 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ASN 2.9 12.4 + - - +
137E TYR* 3.0 43.4 - - - +
139E ARG* 1.3 73.7 - - - +
141E LEU* 1.3 65.1 + - - +
142E GLY* 3.0 5.4 + - - -
118F LEU* 4.2 9.5 - - + +
119F TYR* 5.1 0.2 + - - -
132F PHE* 3.5 33.0 - - + -
136F ASN* 2.6 35.7 + - + +
215F ARG* 4.6 0.9 - - - +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA* 3.4 34.1 - - + +
97E ASP* 3.7 9.0 - - - +
100E LYS* 3.3 46.9 + - + +
137E TYR* 3.0 57.3 + - + +
138E VAL 3.2 6.5 + - - +
140E GLN* 1.3 83.1 - - - +
142E GLY* 1.3 61.9 + - - +
143E LEU* 3.4 8.7 + - + +
118F LEU* 5.7 2.6 - - - +
119F TYR* 4.9 5.9 - - - -
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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