Contacts of the helix formed by residues 128 - 142 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C MET* 3.5 39.7 - - + +
114C PRO* 3.4 14.1 - - + +
116C HIS* 3.5 22.7 - + - -
125C VAL* 2.7 26.0 + - + +
126C PRO 3.3 1.4 + - - -
127C MET* 1.3 103.8 - - - +
129C ALA* 1.3 66.5 + - - +
130C PRO* 3.2 1.8 - - - -
131C LYS* 3.0 23.8 + - - +
261C GLN* 3.6 18.8 - - - +
265C ILE* 4.9 8.1 - - + -
269C PHE* 3.5 34.3 - + - -
276C TYR* 3.2 40.4 + + - -
1353C NAP 3.7 17.8 + + - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO 3.2 9.8 + - - -
115C ASP* 3.4 37.6 - - + +
124C ALA* 3.5 23.3 - - + +
125C VAL 3.1 6.0 + - - +
126C PRO* 5.3 0.4 - - + -
128C TRP* 1.3 76.5 - - - +
130C PRO* 1.3 69.5 - - + +
131C LYS 3.2 0.3 + - - -
132C PHE* 3.4 12.3 + - - +
133C THR* 3.7 10.7 + - - -
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Residues in contact with PRO 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 4.8 18.4 - - + +
89C ILE* 3.7 33.2 - - + +
126C PRO* 3.1 30.3 - - + +
127C MET* 4.3 1.3 - - - -
128C TRP 3.2 6.7 - - - +
129C ALA* 1.3 93.9 - - + +
131C LYS* 1.3 61.8 + - + +
133C THR* 3.2 19.0 + - - +
134C VAL* 3.5 5.9 + - - +
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASN* 3.9 10.4 + - - -
81C THR* 3.0 23.0 + - - +
88C GLU* 2.6 34.9 + - + +
110C TYR* 3.3 22.7 + - - +
111C SER* 3.7 16.0 + - - +
112C SER* 3.9 3.6 - - - -
113C MET* 3.6 38.4 - - + +
127C MET 4.1 11.4 - - - +
128C TRP 3.0 11.4 + - - +
130C PRO* 1.3 75.5 - - + +
132C PHE* 1.3 57.6 + - - +
134C VAL* 2.7 25.4 + - - +
135C GLU 2.9 9.7 + - - -
1353C NAP 3.3 21.5 - - - -
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER* 4.9 0.7 - - - -
113C MET 3.4 19.2 + - - +
114C PRO* 5.3 1.1 - - + -
115C ASP* 4.5 12.8 - - + -
118C LEU* 4.2 26.7 - - + -
119C TYR* 4.3 17.0 - - - -
129C ALA 3.4 10.8 + - - +
131C LYS* 1.3 78.5 - - - +
133C THR* 1.3 63.1 + - - +
135C GLU* 3.5 25.2 - - - +
136C ASN* 3.2 53.0 + - - +
149C TYR* 3.8 13.0 - + - -
215C ARG* 3.8 26.0 - - - -
279C LEU* 5.5 1.3 - - + -
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ILE* 4.2 30.4 - - + +
93C LYS* 4.8 9.2 - - - +
115C ASP* 5.4 2.1 + - - -
129C ALA 3.7 7.9 + - - -
130C PRO* 3.2 13.9 + - - +
131C LYS 3.0 0.6 - - - -
132C PHE* 1.3 81.0 - - - +
134C VAL* 1.3 61.1 + - - +
136C ASN* 3.4 10.5 + - - +
137C TYR* 3.2 18.5 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 3.7 23.8 - - + +
89C ILE* 3.8 20.4 - - + +
92C GLY* 3.8 26.5 - - - +
93C LYS* 4.6 2.5 - - + +
110C TYR* 3.4 35.9 - - + +
130C PRO 3.9 7.9 - - - +
131C LYS* 2.7 12.2 + - - +
133C THR* 1.3 69.9 - - - +
135C GLU* 1.3 66.0 + - - +
137C TYR* 3.2 8.3 + - + +
138C VAL* 3.0 26.5 + - + +
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 4.1 3.1 - - - -
112C SER* 2.9 17.4 + - - -
131C LYS 2.9 10.7 + - - +
132C PHE* 3.5 20.3 - - - +
133C THR 3.2 0.2 - - - -
134C VAL* 1.3 77.4 - - - +
136C ASN* 1.3 65.4 + - - +
138C VAL* 3.0 13.7 + - - +
139C ARG* 2.4 54.3 + - - +
147C PHE* 3.3 36.6 - - + -
149C TYR* 2.7 23.5 + - - -
215C ARG* 2.6 13.5 + - - -
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PHE* 3.2 47.5 + - - +
133C THR* 3.7 9.9 - - - +
134C VAL 3.3 0.2 - - - -
135C GLU* 1.3 80.9 + - - +
137C TYR* 1.3 58.0 + - - +
139C ARG* 3.5 16.6 + - - +
140C GLN* 3.0 26.6 + - - +
215C ARG* 5.3 2.0 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLY 4.9 0.7 - - - -
93C LYS* 3.6 57.6 - - + +
96C ALA* 3.9 12.3 - - + -
97C ASP* 2.5 36.8 + - - -
133C THR 3.2 10.1 + - - +
134C VAL* 3.2 13.9 + - - +
135C GLU 3.1 0.4 - - - -
136C ASN* 1.3 77.1 - - - +
138C VAL* 1.3 66.8 + - - +
140C GLN* 3.0 27.5 + - - +
141C LEU* 3.0 43.1 + - + +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA* 4.1 23.1 - - + -
108C TYR* 4.1 23.1 - - + +
110C TYR* 4.9 2.2 - - + -
134C VAL* 3.0 27.1 + - + +
135C GLU 3.0 7.4 + - - +
137C TYR* 1.3 78.8 - - + +
139C ARG* 1.3 61.4 + - - +
141C LEU* 3.3 12.5 + - - +
142C GLY 3.3 7.4 + - - -
143C LEU* 3.5 21.0 + - + +
145C SER* 3.6 29.2 - - - +
147C PHE* 3.7 15.0 - - + -
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLU* 2.4 49.1 + - - +
136C ASN* 3.7 15.6 - - - +
138C VAL* 1.3 76.9 - - - +
140C GLN* 1.3 62.8 + - - +
142C GLY* 3.1 15.4 + - - +
143C LEU 5.3 1.1 - - - +
145C SER* 4.9 4.0 - - - +
147C PHE* 3.6 22.7 - - + -
213C GLY* 2.7 34.9 + - - -
215C ARG* 2.8 34.6 - - - +
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Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASN 3.0 14.7 + - - +
137C TYR* 3.0 38.6 + - + +
139C ARG* 1.3 78.3 - - - +
141C LEU* 1.3 61.3 + - + +
142C GLY* 3.1 1.2 + - - -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA* 3.4 33.4 - - + +
97C ASP* 3.5 17.5 - - - +
100C LYS* 3.6 53.2 + - + +
137C TYR* 3.0 38.1 + - + +
138C VAL 3.3 8.5 + - - +
140C GLN* 1.3 78.8 - - + +
142C GLY* 1.3 60.7 + - - +
143C LEU* 3.5 8.2 + - + +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL 3.3 0.4 + - - -
139C ARG* 3.1 13.3 + - - -
140C GLN 3.0 6.8 - - - -
141C LEU* 1.3 80.0 - - - +
143C LEU* 1.3 64.9 + - - +
144C PRO* 3.4 5.5 - - - +
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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