Contacts of the helix formed by residues 128 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B MET* 3.4 40.5 - - + +
114B PRO* 3.5 14.1 - - + +
116B HIS* 3.8 27.4 - + - -
125B VAL* 2.9 36.3 + - + +
126B PRO 3.2 0.4 - - - -
127B MET* 1.3 92.3 - - + +
129B ALA* 1.3 67.9 + - - +
130B PRO* 3.1 2.7 - - - -
131B LYS* 2.8 24.1 + - - +
261B GLN* 3.7 19.0 - - - +
265B ILE* 5.1 9.2 - - + -
269B PHE* 4.1 14.8 - + - -
276B TYR* 3.4 41.3 - + - -
1353B NAP 3.7 20.9 + + - -
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Residues in contact with ALA 129 (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 PRO 3.4 10.7 + - - -
115B ASP* 3.6 24.1 - - + +
124B ALA* 3.6 32.3 - - + -
125B VAL 2.8 13.0 + - - +
126B PRO* 5.0 0.9 - - + -
128B TRP* 1.3 72.2 - - - +
130B PRO* 1.3 68.4 - - + +
132B PHE* 3.1 20.3 + - - +
133B THR* 3.7 6.6 + - - -
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 4.6 20.6 - - + +
89B ILE* 3.9 24.9 - - + +
126B PRO* 3.2 26.9 - - + +
127B MET* 4.3 4.0 - - - -
128B TRP 3.2 4.7 - - - +
129B ALA* 1.3 96.2 - - + +
131B LYS* 1.3 63.2 + - - +
133B THR* 3.0 23.6 + - - +
134B VAL* 3.3 11.2 + - - +
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Residues in contact with LYS 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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80B ASN* 4.3 6.1 + - - -
81B THR* 2.8 30.9 + - - +
88B GLU* 2.6 33.6 + - - +
110B TYR* 3.4 22.1 + - + +
111B SER* 3.9 17.5 + - - +
112B SER* 3.7 7.8 + - - -
113B MET* 3.4 39.3 - - + +
127B MET 4.1 9.9 - - - +
128B TRP 2.8 15.1 + - - +
130B PRO* 1.3 74.5 - - - +
132B PHE* 1.3 61.8 + - - +
134B VAL* 3.2 2.5 + - - -
135B GLU 3.1 17.3 + - - -
1353B NAP 3.2 27.8 - - - -
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Residues in contact with PHE 132 (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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112B SER* 4.0 3.8 - - - -
113B MET 3.4 18.0 + - - +
114B PRO* 4.9 2.2 - - + -
115B ASP* 4.1 11.2 - - + -
118B LEU* 3.7 31.9 - - + -
119B TYR* 3.8 16.2 - - - -
129B ALA 3.1 12.3 + - - +
130B PRO 3.1 0.6 - - - -
131B LYS* 1.3 76.3 - - - +
133B THR* 1.3 66.2 + - - +
135B GLU* 3.4 8.5 + - - +
136B ASN* 3.4 23.0 + - + +
149B TYR* 3.5 22.2 - + - -
215B ARG* 3.4 32.5 - - - -
279B LEU* 4.4 5.8 - - + -
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Residues in contact with THR 133 (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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89B ILE* 4.2 30.1 - - + +
93B LYS* 5.1 7.9 - - - +
115B ASP* 5.2 3.1 + - - -
129B ALA 3.7 7.5 + - - -
130B PRO* 3.0 13.5 + - - +
132B PHE* 1.3 80.5 - - - +
134B VAL* 1.3 62.3 + - - +
136B ASN* 3.3 9.7 + - - +
137B TYR* 3.2 17.8 + - - +
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Residues in contact with VAL 134 (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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88B GLU 3.5 8.7 - - - +
89B ILE* 3.5 42.2 - - + +
92B GLY* 3.5 31.0 - - - +
93B LYS* 4.2 4.7 - - + +
110B TYR* 3.6 29.2 - - + +
130B PRO 3.3 6.7 + - - +
131B LYS 3.2 2.9 + - - +
133B THR* 1.3 74.3 - - - +
135B GLU* 1.3 65.2 + - - +
137B TYR* 3.2 7.7 + - + +
138B VAL* 2.9 27.3 + - + +
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Residues in contact with GLU 135 (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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110B TYR* 4.0 4.0 - - + -
112B SER* 2.9 20.5 + - - +
131B LYS 3.1 6.2 + - - +
132B PHE* 3.5 12.9 - - - +
133B THR 3.2 0.2 - - - -
134B VAL* 1.3 77.5 - - - +
136B ASN* 1.3 63.4 + - - +
138B VAL* 3.1 5.5 + - - +
139B ARG* 2.6 53.4 + - - +
147B PHE* 3.1 43.3 - - + -
149B TYR* 2.4 27.7 + - - -
215B ARG* 2.9 18.2 + - - -
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Residues in contact with ASN 136 (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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132B PHE* 3.4 11.5 + - + +
133B THR* 3.3 11.1 + - - +
135B GLU* 1.3 81.7 - - - +
137B TYR* 1.3 57.2 + - - +
139B ARG* 3.6 17.9 + - - +
140B GLN* 3.0 36.0 + - - +
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Residues in contact with TYR 137 (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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92B GLY 5.0 0.4 - - - -
93B LYS* 3.6 53.2 - - + -
96B ALA* 3.9 11.7 - - + -
97B ASP* 2.4 40.0 + - - -
133B THR 3.2 12.0 + - - +
134B VAL* 3.2 12.9 + - + +
135B GLU 3.1 0.6 - - - -
136B ASN* 1.3 77.1 - - - +
138B VAL* 1.3 68.6 + - - +
140B GLN* 3.1 33.5 - - - +
141B LEU* 3.0 43.6 + - + +
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Residues in contact with VAL 138 (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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96B ALA* 4.2 16.6 - - + -
108B TYR* 4.0 28.3 - - + +
110B TYR* 4.7 3.1 - - + -
134B VAL* 2.9 28.1 + - + +
135B GLU 3.3 8.1 - - - +
137B TYR* 1.3 77.7 - - - +
139B ARG* 1.3 64.5 + - - +
141B LEU* 3.0 15.6 + - - +
142B GLY 3.2 7.3 + - - -
143B LEU* 3.6 19.8 + - + +
145B SER* 3.7 19.5 - - - +
147B PHE* 3.7 23.3 - - + -
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Residues in contact with ARG 139 (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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135B GLU* 2.6 47.7 + - - +
136B ASN* 3.6 20.5 + - - +
138B VAL* 1.3 76.4 - - - +
140B GLN* 1.3 63.2 + - - +
142B GLY* 3.0 15.8 + - - +
143B LEU 5.3 1.1 - - - +
145B SER* 4.9 4.9 - - - +
147B PHE* 3.7 15.2 - - + -
213B GLY* 2.9 41.0 + - - -
215B ARG* 3.3 29.9 - - - +
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Residues in contact with GLN 140 (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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136B ASN* 3.0 25.7 + - - +
137B TYR* 3.1 40.8 - - - +
139B ARG* 1.3 78.1 - - - +
141B LEU* 1.3 63.1 + - - +
142B GLY* 3.2 1.4 + - - -
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Residues in contact with LEU 141 (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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96B ALA* 3.3 30.5 - - + +
97B ASP* 3.3 21.3 - - - +
100B LYS* 3.0 52.3 + - + +
137B TYR* 3.0 44.3 + - + +
138B VAL 3.0 8.0 + - - +
140B GLN* 1.3 76.9 - - - +
142B GLY* 1.3 58.2 + - - +
143B LEU* 3.3 10.1 - - + -
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Residues in contact with GLY 142 (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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100B LYS* 5.2 2.1 + - - -
138B VAL 3.2 0.4 + - - -
139B ARG 3.0 18.3 + - - -
140B GLN 3.0 1.7 - - - -
141B LEU* 1.3 79.8 - - - +
143B LEU* 1.3 64.9 + - - +
144B PRO* 3.5 4.9 - - - +
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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