Contacts of the helix formed by residues 128 - 142 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113G MET* 3.5 39.5 - - + +
114G PRO* 3.4 13.3 - - + +
116G HIS* 3.6 28.5 - + - -
125G VAL* 2.8 36.3 + - + +
126G PRO 3.3 0.8 - - - -
127G MET* 1.3 104.9 - - + +
129G ALA* 1.3 69.8 + - - +
130G PRO* 3.1 2.0 - - - -
131G LYS* 2.8 24.8 + - - +
132G PHE 3.9 1.2 + - - -
261G GLN* 3.7 19.2 - - - +
265G ILE* 4.6 12.1 - - + -
269G PHE* 4.0 14.8 - + - -
276G TYR* 3.5 35.7 - + - -
1353G NAP 3.7 21.2 + + - -
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G PRO 3.0 12.9 + - - -
115G ASP* 3.6 22.3 - - + +
124G ALA* 3.5 32.5 - - + -
125G VAL 3.0 6.9 + - - +
126G PRO* 5.4 0.4 - - + -
128G TRP* 1.3 76.3 - - - +
130G PRO* 1.3 65.5 - - + +
132G PHE* 2.9 30.0 + - - +
133G THR* 3.7 4.4 + - - -
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Residues in contact with PRO 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU* 5.0 15.9 - - + +
89G ILE* 3.5 32.2 - - + +
126G PRO* 3.5 27.1 - - + +
127G MET* 4.3 0.9 - - - -
128G TRP 3.1 7.0 - - - +
129G ALA* 1.3 95.0 - - + +
131G LYS* 1.3 60.6 + - + +
133G THR* 3.3 21.5 - - - +
134G VAL* 3.5 5.4 + - - +
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Residues in contact with LYS 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G ASN* 3.7 14.0 + - - -
81G THR* 2.8 33.7 + - - +
88G GLU* 3.0 27.3 + - + +
110G TYR* 3.3 26.6 + - - +
111G SER 3.8 13.3 + - - +
112G SER* 3.6 5.8 + - - -
113G MET* 3.8 34.5 - - + +
127G MET 4.2 9.2 - - - +
128G TRP 2.8 16.8 + - - +
130G PRO* 1.3 70.8 - - + +
132G PHE* 1.3 66.0 + - - +
134G VAL* 3.1 2.8 + - - -
135G GLU 3.0 17.3 + - - -
1353G NAP 3.2 24.7 - - - -
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Residues in contact with PHE 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G SER* 3.7 7.4 - - - -
113G MET 3.6 14.1 + - - +
114G PRO* 5.7 0.9 - - + -
115G ASP* 4.4 10.8 - - + -
118G LEU* 3.7 29.2 - - + -
119G TYR* 4.3 17.0 - - - -
129G ALA 2.9 13.0 + - - +
131G LYS* 1.3 78.2 - - - +
133G THR* 1.3 66.3 + - - +
135G GLU* 2.9 27.4 + - - +
136G ASN* 3.1 34.4 + - - +
149G TYR* 3.9 15.7 - - - -
215G ARG* 3.5 28.9 - - - -
279G LEU* 5.7 0.9 - - + -
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Residues in contact with THR 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ILE* 4.1 29.7 - - + +
93G LYS* 5.0 9.0 - - - +
115G ASP* 5.5 2.6 + - - -
129G ALA 3.7 5.9 + - - -
130G PRO* 3.3 15.0 + - - +
132G PHE* 1.3 82.8 - - - +
134G VAL* 1.3 61.9 + - - +
136G ASN* 3.4 11.5 + - - +
137G TYR* 3.2 19.2 + - - +
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Residues in contact with VAL 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 3.6 22.4 - - - +
89G ILE* 3.8 15.9 - - + +
92G GLY* 3.8 24.7 - - - +
93G LYS* 4.5 2.5 - - + +
96G ALA* 5.7 0.2 - - + -
108G TYR* 6.1 0.4 - - - +
110G TYR* 3.4 43.7 - - + +
130G PRO 3.7 12.8 - - - +
131G LYS* 3.1 2.7 + - - +
133G THR* 1.3 74.2 - - - +
135G GLU* 1.3 67.4 + - - +
137G TYR* 3.0 9.3 + - + +
138G VAL* 2.9 27.3 + - + +
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G TYR* 4.2 2.8 - - - -
112G SER* 3.0 20.9 + - - +
131G LYS 3.0 11.0 + - - +
132G PHE* 2.9 18.6 + - - +
134G VAL* 1.3 77.0 - - - +
136G ASN* 1.3 65.6 + - - +
138G VAL* 3.0 14.4 + - - +
139G ARG* 2.9 43.3 + - - +
147G PHE* 3.5 23.3 - - + +
149G TYR* 2.6 30.1 + - - -
215G ARG* 2.8 33.8 + - - -
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Residues in contact with ASN 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G PHE* 3.1 49.4 + - - +
133G THR* 3.7 9.8 - - - +
135G GLU* 1.3 79.3 + - - +
137G TYR* 1.3 57.1 + - - +
139G ARG* 3.3 20.2 + - - +
140G GLN* 2.8 29.4 + - - +
215G ARG* 4.9 2.2 - - - +
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Residues in contact with TYR 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G GLY 5.6 0.2 - - - -
93G LYS* 3.7 52.9 - - + +
96G ALA* 4.1 8.7 - - + -
97G ASP* 2.7 38.0 + - - -
133G THR 3.2 10.7 + - - +
134G VAL* 3.0 14.2 + - + +
136G ASN* 1.3 76.7 - - - +
138G VAL* 1.3 65.9 + - - +
140G GLN* 3.2 28.6 + - - +
141G LEU* 3.0 47.1 + - + +
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Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ALA* 4.2 21.3 - - + -
108G TYR* 4.2 17.9 - - + +
110G TYR* 4.8 1.8 - - + -
134G VAL* 2.9 27.7 + - + +
135G GLU 3.0 7.2 + - - +
137G TYR* 1.3 78.1 - - - +
139G ARG* 1.3 63.7 + - - +
141G LEU* 3.0 14.5 + - - +
142G GLY 3.3 7.4 + - - -
143G LEU* 3.5 21.8 + - + -
145G SER* 3.4 30.1 - - - +
147G PHE* 3.6 17.0 - - + -
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Residues in contact with ARG 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G GLU* 2.9 35.5 + - - +
136G ASN* 3.4 22.2 - - - +
138G VAL* 1.3 76.6 - - - +
140G GLN* 1.3 62.5 + - - +
142G GLY* 3.0 14.9 + - - -
143G LEU 5.3 1.1 - - - +
145G SER* 4.9 3.8 - - - +
147G PHE* 2.8 41.8 - - + -
213G GLY* 2.9 34.6 + - - -
215G ARG* 4.2 20.3 - - - +
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Residues in contact with GLN 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ASN 2.8 14.9 + - - +
137G TYR* 3.3 37.0 - - - +
138G VAL 3.1 0.4 - - - -
139G ARG* 1.3 73.3 - - - +
141G LEU* 1.3 69.8 + - - +
142G GLY* 3.0 6.4 + - - -
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Residues in contact with LEU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ALA* 3.5 30.7 - - + +
97G ASP* 3.4 11.9 - - - +
100G LYS* 3.4 44.5 - - + +
137G TYR* 3.0 52.1 + - + +
138G VAL 3.0 7.5 + - - +
140G GLN* 1.3 83.7 - - - +
142G GLY* 1.3 61.9 + - - +
143G LEU* 3.5 9.0 + - + +
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G VAL 3.3 0.2 + - - -
139G ARG* 3.0 12.4 + - - -
140G GLN 3.0 7.0 + - - -
141G LEU* 1.3 80.2 - - - +
143G LEU* 1.3 64.7 + - - +
144G PRO* 3.5 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