Contacts of the helix formed by residues 114 - 124 (chain C) in PDB entry 3VZC
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 ASN 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C SER 2.9 25.8 - - - +
80C GLY* 3.8 2.6 - - - -
81C ASP* 3.7 3.6 - - - +
109C PRO* 3.4 26.4 - - + +
110C ALA 3.3 6.7 + - - -
111C GLY 2.5 33.1 + - - -
112C SER* 3.6 4.4 - - - +
113C GLY* 1.3 77.2 - - - +
115C ALA* 1.3 57.4 + - - +
116C LEU 3.4 2.2 - - - -
117C ALA* 3.5 5.7 + - + +
118C ALA* 2.9 30.5 + - - +
134C LEU* 4.6 8.3 - - + +
269C GLY* 5.1 3.2 - - - -
270C SER* 4.4 9.6 + - - +
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Residues in contact with ALA 115 (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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81C ASP* 3.0 14.8 + - - +
114C ASN* 1.3 73.5 - - - +
116C LEU* 1.3 61.8 + - - +
118C ALA* 3.2 3.6 + - - +
119C SER* 2.8 35.8 + - - -
167C LEU* 3.8 16.2 - - + -
267C HIS* 3.3 17.7 - - - +
268C LEU 3.3 25.6 - - - +
269C GLY* 4.0 10.0 - - - +
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Residues in contact with LEU 116 (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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81C ASP* 2.9 18.2 + - + +
84C MET* 3.5 37.5 - - + -
107C SER* 4.4 6.7 - - - +
115C ALA* 1.3 76.2 - - - +
117C ALA* 1.3 63.4 + - - +
119C SER* 3.2 5.9 + - - -
120C LEU* 3.0 31.7 + - + +
166C VAL* 4.0 19.5 - - + +
167C LEU* 4.1 8.2 - - + +
265C HIS* 3.6 39.9 - - + +
361C MET* 3.9 31.4 - - + -
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Residues in contact with ALA 117 (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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81C ASP* 4.5 0.4 + - - -
107C SER* 3.8 26.3 + - - +
109C PRO* 4.0 21.8 - - + -
114C ASN* 3.5 11.3 + - + +
115C ALA 3.4 0.2 - - - -
116C LEU* 1.3 78.2 - - - +
118C ALA* 1.3 56.7 + - - +
120C LEU* 3.4 5.3 + - - +
121C ASN* 2.9 29.5 + - - +
134C LEU* 4.6 2.2 - - + -
138C CYS* 3.6 28.0 - - - -
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Residues in contact with ALA 118 (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 ASN 2.9 19.2 + - - +
115C ALA 3.2 4.5 + - - +
117C ALA* 1.3 73.4 - - - +
119C SER* 1.3 60.7 + - - +
121C ASN* 3.4 8.5 - - - +
122C HIS* 3.0 27.0 + - - +
128C GLN* 6.5 0.2 - - + -
134C LEU* 4.3 7.6 - - + -
267C HIS* 4.1 9.7 + - + -
269C GLY 4.0 5.8 - - - +
270C SER* 3.4 34.8 - - - +
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Residues in contact with SER 119 (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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115C ALA 2.8 22.6 + - - -
116C LEU 3.4 5.6 - - - -
118C ALA* 1.3 74.3 - - - +
120C LEU* 1.3 59.6 + - - +
122C HIS* 3.1 2.6 + - - +
123C TYR* 2.9 43.5 + - - -
265C HIS* 3.4 24.1 - - - +
266C SER* 3.4 16.8 - - - -
267C HIS* 3.1 26.9 + - - +
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Residues in contact with LEU 120 (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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107C SER* 4.6 12.3 - - - +
116C LEU* 3.0 28.0 + - + +
117C ALA* 3.8 5.6 - - - +
119C SER* 1.3 72.6 - - - +
121C ASN* 1.3 65.7 + - - +
123C TYR* 3.5 22.8 + - + +
124C ALA* 3.2 23.0 + - - +
138C CYS* 5.7 1.3 - - - -
141C LEU* 4.0 13.2 - - + +
150C MET* 4.2 21.1 - - - -
265C HIS* 5.1 3.6 - - + -
279C ARG* 5.5 0.2 - - - +
361C MET* 3.8 26.0 - - + -
362C VAL 3.8 18.2 - - - +
363C SER* 4.0 22.2 - - - -
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Residues in contact with ASN 121 (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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117C ALA 2.9 17.7 + - - +
118C ALA 3.4 6.8 - - - +
120C LEU* 1.3 76.5 - - - +
122C HIS* 1.3 64.1 + - - +
124C ALA* 3.2 12.2 + - - +
125C GLY 3.4 0.3 + - - -
126C TYR* 3.1 31.5 + - - +
127C GLU 3.0 24.8 - - - +
128C GLN* 4.6 2.3 - - - -
129C VAL* 3.8 7.6 + - - +
134C LEU* 3.6 19.7 - - + +
137C ASN* 3.0 38.3 - - - +
138C CYS* 4.7 3.5 - - - +
141C LEU* 4.6 5.0 - - - +
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Residues in contact with HIS 122 (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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118C ALA 3.0 8.9 + - - +
119C SER 3.1 6.9 + - - +
121C ASN* 1.3 76.8 - - - +
123C TYR* 1.3 65.0 + + - +
125C GLY* 2.9 22.5 + - - -
126C TYR 4.5 12.1 - - - -
128C GLN* 5.5 5.8 - - + -
266C SER* 4.0 13.6 + - - -
267C HIS* 3.5 28.7 - + + -
273C PHE* 3.4 34.8 - + - -
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Residues in contact with TYR 123 (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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119C SER* 2.9 21.8 + - - +
120C LEU* 3.8 24.0 - - + +
122C HIS* 1.3 82.6 - + - +
124C ALA* 1.3 59.7 + - - +
125C GLY* 3.5 0.7 + - - -
150C MET* 4.6 0.9 - - + -
264C LEU 4.5 1.2 + - - -
265C HIS* 2.8 40.0 + + - -
266C SER* 3.1 41.0 + - - -
279C ARG* 3.7 69.4 + - + +
280C CYS 5.3 1.0 + - - -
363C SER* 5.8 2.5 - - - -
364C GLY 3.8 10.9 - - - +
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Residues in contact with ALA 124 (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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120C LEU 3.2 16.4 + - - +
121C ASN 3.6 6.1 - - - +
122C HIS 3.1 1.6 - - - -
123C TYR* 1.3 76.3 - - - +
125C GLY* 1.3 60.1 + - - +
126C TYR* 3.6 15.9 + - + -
141C LEU* 3.9 27.6 - - + -
364C GLY* 3.8 19.4 + - - +
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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