Contacts of the helix formed by residues 128 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F MET* 3.4 43.0 - - + +
114F PRO* 3.3 16.8 - - + +
116F HIS* 3.7 17.7 - + - -
125F VAL* 3.0 38.9 + - + -
126F PRO 3.4 0.4 - - - -
127F MET* 1.3 89.5 - - + +
129F ALA* 1.3 68.0 + - - +
130F PRO* 3.3 2.7 - - - -
131F LYS* 3.0 23.2 + - - +
261F GLN* 4.1 17.7 - - - +
265F ILE* 5.0 7.9 - - + -
269F PHE* 3.5 31.9 - + - -
276F TYR* 3.4 36.3 - + - -
1353F NAP 3.9 20.4 + + - -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F PRO 3.2 10.4 + - - -
115F ASP* 3.7 33.1 - - + +
124F ALA* 4.0 15.5 - - + +
125F VAL 3.0 10.3 + - - +
126F PRO* 5.4 0.4 - - + -
128F TRP* 1.3 78.3 - - - +
130F PRO* 1.3 69.1 - - + +
132F PHE* 3.0 20.6 + - - +
133F THR* 3.6 6.5 + - - -
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Residues in contact with PRO 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLU* 4.9 15.7 - - + +
89F ILE* 3.6 31.2 - - + +
126F PRO* 3.2 28.0 - - + +
127F MET* 4.2 1.6 - - - -
128F TRP 3.3 5.4 - - - +
129F ALA* 1.3 94.3 - - + +
131F LYS* 1.3 61.8 + - + +
133F THR* 3.0 22.9 + - - +
134F VAL* 3.4 5.0 + - - +
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Residues in contact with LYS 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASN* 3.7 11.1 + - - -
81F THR* 2.8 35.8 + - - +
88F GLU* 3.0 25.2 + - - +
110F TYR* 3.2 37.3 + - - +
111F SER 4.2 11.7 + - - +
112F SER* 3.4 7.2 + - - -
113F MET* 3.9 28.5 - - + +
127F MET 3.9 17.0 - - - +
128F TRP 3.0 12.4 + - - +
130F PRO* 1.3 80.0 - - - +
132F PHE* 1.3 59.2 + - - +
134F VAL* 3.3 2.0 + - - +
135F GLU 3.2 6.9 + - - -
1353F NAP 3.0 30.7 - - - -
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Residues in contact with PHE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ARG 4.4 0.4 - - - -
140E GLN* 3.5 39.0 - - + -
142E GLY 5.6 0.2 - - - -
112F SER* 3.7 6.5 - - - -
113F MET 3.3 15.1 + - - +
114F PRO* 4.8 5.2 - - + -
115F ASP* 4.3 12.8 - - + -
118F LEU* 3.9 20.6 - - + -
119F TYR* 4.2 17.3 - - - -
128F TRP 3.6 0.8 + - - -
129F ALA 3.0 15.7 + - - +
131F LYS* 1.3 76.7 - - - +
133F THR* 1.3 65.4 + - - +
135F GLU* 3.2 34.3 - - + +
136F ASN* 3.4 8.9 + - + +
149F TYR* 3.6 19.1 - - - -
215F ARG* 3.7 18.4 - - - -
279F LEU* 5.4 0.9 - - + -
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Residues in contact with THR 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ILE* 4.0 27.0 - - + +
93F LYS* 5.2 8.3 - - - +
129F ALA 3.6 6.8 + - - -
130F PRO* 3.0 14.0 + - - +
132F PHE* 1.3 78.1 - - - +
134F VAL* 1.3 66.1 + - - +
136F ASN* 3.5 8.2 + - + +
137F TYR* 3.3 18.5 + - - +
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F GLU 3.5 24.9 - - - +
89F ILE* 3.7 20.2 - - + +
92F GLY* 3.6 28.0 - - - +
93F LYS* 4.5 2.0 - - + +
96F ALA* 5.5 0.2 - - + -
110F TYR* 3.4 37.7 - - + +
130F PRO 3.4 7.8 + - - +
131F LYS* 3.3 1.7 + - - +
132F PHE 3.3 0.4 - - - -
133F THR* 1.3 74.8 - - - +
135F GLU* 1.3 65.9 + - - +
137F TYR* 3.0 9.9 + - + +
138F VAL* 2.9 28.6 + - + +
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 3.9 3.5 - - - -
112F SER* 2.7 30.8 + - - +
131F LYS 3.2 3.8 + - - +
132F PHE* 3.2 17.2 - - + +
134F VAL* 1.3 78.7 - - - +
136F ASN* 1.3 63.2 + - - +
138F VAL* 3.2 5.9 + - - +
139F ARG* 3.1 31.2 + - - +
147F PHE* 3.4 40.2 - - + -
149F TYR* 2.5 24.5 + - - -
215F ARG* 2.8 40.6 + - - -
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Residues in contact with ASN 136 (chain F).
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* 4.0 23.0 - - - +
140E GLN* 2.6 49.3 + - + +
132F PHE* 3.4 10.4 + - + +
133F THR* 3.7 10.5 - - - +
135F GLU* 1.3 80.4 - - - +
137F TYR* 1.3 57.9 + - - +
139F ARG* 3.2 13.3 + - - +
140F GLN* 2.8 31.9 + - - +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LYS* 3.9 51.8 - - + -
96F ALA* 4.0 8.5 - - + -
97F ASP* 2.8 29.3 + - - -
133F THR 3.3 10.1 + - - +
134F VAL* 3.0 13.9 + - + +
136F ASN* 1.3 77.3 - - - +
138F VAL* 1.3 66.8 + - - +
140F GLN* 3.0 31.3 + - - +
141F LEU* 2.9 55.7 + - + +
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ALA* 4.2 13.0 - - + -
108F TYR* 3.8 31.9 - - + -
110F TYR* 4.7 2.5 - - + -
134F VAL* 2.9 26.8 + - + +
135F GLU 3.2 8.3 + - - +
137F TYR* 1.3 77.3 - - - +
139F ARG* 1.3 65.5 + - - +
141F LEU* 3.1 17.6 + - - +
142F GLY 3.3 7.4 + - - -
143F LEU* 3.5 15.8 + - + +
145F SER* 3.5 30.5 - - - +
147F PHE* 3.6 13.9 - - + -
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Residues in contact with ARG 139 (chain F).
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* 3.7 8.4 - - - -
136E ASN* 3.4 35.2 - - - +
139E ARG* 3.6 30.9 - - - +
215E ARG* 5.3 3.3 - - - +
135F GLU* 3.1 29.3 + - - +
136F ASN* 3.2 17.4 + - - +
138F VAL* 1.3 81.2 - - - +
140F GLN* 1.3 62.9 + - - +
142F GLY* 3.0 15.1 + - - +
143F LEU 5.3 1.1 - - - +
145F SER* 5.0 3.1 - - - +
147F PHE* 3.6 18.9 - - + -
213F GLY* 3.0 40.6 + - - -
215F ARG* 3.4 43.2 - - - +
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Residues in contact with GLN 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E LEU* 4.0 14.6 - - - +
132E PHE* 4.5 3.2 - - - -
136E ASN* 4.0 10.3 - - + -
136F ASN* 2.8 17.4 + - - +
137F TYR* 3.0 37.4 + - + +
139F ARG* 1.3 78.7 - - - +
141F LEU* 1.3 65.4 + - + +
142F GLY 3.0 1.0 + - - -
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E LEU* 4.0 8.0 - - - +
96F ALA* 3.4 37.9 - - + +
97F ASP* 3.7 8.1 - - - +
100F LYS* 2.8 50.5 + - + +
137F TYR* 2.9 57.3 + - + +
138F VAL* 3.1 6.9 + - - +
140F GLN* 1.3 79.7 - - - +
142F GLY* 1.3 60.8 + - - +
143F LEU* 4.0 11.0 - - + -
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Residues in contact with GLY 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E LEU* 4.2 25.3 - - - +
119E TYR* 4.9 10.1 - - - -
132E PHE* 4.9 5.4 - - - -
138F VAL 3.3 0.4 + - - -
139F ARG 3.0 13.5 + - - -
140F GLN 3.0 6.8 - - - -
141F LEU* 1.3 80.5 - - - +
143F LEU* 1.3 63.2 + - - +
144F PRO* 3.6 6.8 - - - +
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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