Contacts of the helix formed by residues 141 - 153 (chain C) in PDB entry 2VZE
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 LYS 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C GLN* 3.3 19.3 - - - +
140C MET* 1.3 76.4 - - - +
142C SER* 1.3 67.8 + - - +
143C THR 3.3 1.3 - - - -
144C ASP* 2.9 20.4 + - - +
145C ILE* 3.1 14.9 + - - +
166C GLU* 3.4 23.5 + - + +
532C LYS 3.7 15.9 + - - -
533C SER* 3.3 24.9 + - - +
534C VAL* 3.2 22.2 - - - +
535C THR 3.5 19.1 - - - +
537C PRO* 5.0 5.0 - - - +
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Residues in contact with SER 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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141C LYS* 1.3 72.8 - - - +
143C THR* 1.3 61.8 + - - +
145C ILE* 3.1 5.3 + - - +
146C LEU* 2.7 31.4 + - - +
166C GLU* 2.8 48.1 + - - -
169C THR* 4.1 15.6 - - - +
170C VAL* 3.9 16.3 - - - +
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Residues in contact with THR 143 (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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141C LYS 3.3 0.8 - - - -
142C SER* 1.3 80.0 + - - +
144C ASP* 1.3 67.4 + - - +
146C LEU* 3.8 10.6 - - + +
147C TYR* 3.1 24.8 + - + +
170C VAL* 5.7 0.2 - - - -
484C GLU* 3.6 28.7 + - - +
534C VAL* 3.9 15.6 + - - +
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Residues in contact with ASP 144 (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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140C MET* 3.5 15.1 - - + +
141C LYS 2.9 27.2 + - - +
143C THR* 1.3 82.3 - - - +
145C ILE* 1.3 62.3 + - - +
147C TYR* 3.5 3.4 + - - +
148C ARG* 3.2 50.8 + - - +
534C VAL 4.0 1.9 - - - +
535C THR* 2.5 27.7 + - - -
536C ALA* 3.0 20.1 + - - +
539C LYS* 4.3 5.1 + - - -
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Residues in contact with ILE 145 (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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140C MET* 3.7 26.7 - - + +
141C LYS 3.1 16.7 + - - +
142C SER* 3.1 5.3 + - - +
144C ASP* 1.3 74.5 - - - +
146C LEU* 1.3 67.8 + - - +
148C ARG* 3.1 5.8 + - + -
149C LEU* 2.9 48.0 + - + +
157C ILE* 4.5 5.8 - - + -
163C VAL* 4.0 13.9 - - + -
166C GLU* 3.8 27.8 - - + -
167C VAL* 3.9 28.7 - - + +
170C VAL* 4.4 7.9 - - + -
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Residues in contact with LEU 146 (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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142C SER 2.7 19.8 + - - +
143C THR* 3.8 10.3 - - + +
145C ILE* 1.3 72.2 - - - +
147C TYR* 1.3 58.1 + - - +
149C LEU* 4.0 0.7 - - - +
150C GLN* 2.9 75.8 + - + +
170C VAL* 4.0 20.6 - - + +
173C GLU* 3.9 31.2 - - + +
174C CYS* 3.8 17.3 - - - -
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Residues in contact with TYR 147 (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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143C THR* 3.1 18.4 + - + +
144C ASP* 3.7 4.3 - - - +
146C LEU* 1.3 79.7 - - - +
148C ARG* 1.3 71.1 + - + +
150C GLN* 4.1 3.5 - - - +
151C MET* 3.0 68.1 + - + +
220C PHE* 3.9 15.3 - + - -
227C LEU* 3.5 43.9 + - + +
228C PRO* 2.6 43.7 + - + -
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Residues in contact with ARG 148 (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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134C MET* 5.7 1.3 - - + -
136C GLY* 5.4 4.5 - - - -
140C MET* 3.6 32.2 - - - +
144C ASP* 3.2 39.9 + - - +
145C ILE* 3.1 5.6 + - - +
147C TYR* 1.3 81.8 - - + +
149C LEU* 1.3 60.9 + - + +
152C SER* 2.7 38.4 + - - -
220C PHE* 3.5 55.6 + - + +
228C PRO* 4.2 21.2 - - - +
477C GLU* 5.2 0.6 + - - -
538C TYR* 4.9 10.1 + - - -
539C LYS* 5.0 7.1 - - - +
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Residues in contact with LEU 149 (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 ALA* 4.0 20.6 - - + -
134C MET* 5.3 0.4 - - + -
145C ILE* 2.9 38.7 + - + +
146C LEU 5.2 0.2 - - - +
148C ARG* 1.3 77.9 - - + +
150C GLN* 1.3 59.2 + - - +
152C SER* 3.4 3.4 + - - +
153C LYS* 2.9 29.3 + - - -
154C ALA* 3.4 27.9 + - + +
157C ILE* 4.5 12.3 - - + -
167C VAL* 5.0 4.3 - - + -
170C VAL* 5.3 2.5 - - + -
171C ALA* 5.6 1.1 - - - -
174C CYS* 3.9 30.5 - - + +
177C LEU* 4.1 25.4 - - + -
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Residues in contact with GLN 150 (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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146C LEU* 2.9 48.7 + - + +
147C TYR* 4.1 3.7 - - - +
149C LEU* 1.3 78.3 - - - +
151C MET* 1.3 64.7 + - + +
153C LYS* 3.5 17.0 + - - +
173C GLU* 2.9 31.0 + - - +
174C CYS* 4.2 7.6 - - - -
175C PRO* 5.4 4.4 - - + +
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Residues in contact with MET 151 (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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108C ARG* 4.8 1.6 + - - -
147C TYR* 3.0 65.5 + - + +
148C ARG 4.2 2.0 - - - +
150C GLN* 1.3 78.5 - - + +
152C SER* 1.3 59.7 + - - +
153C LYS* 4.8 3.8 - - - +
220C PHE* 4.4 6.1 - - + -
228C PRO 4.4 4.5 - - - +
229C LYS* 5.8 2.0 - - - -
230C MET* 3.6 37.8 - - + +
428C ASP* 4.4 6.1 - - - +
429C ASN* 6.1 3.6 - - - +
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Residues in contact with SER 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ARG* 3.0 30.8 + - - +
134C MET* 3.3 36.3 - - - +
148C ARG 2.7 22.0 + - - -
149C LEU 3.4 1.4 + - - -
151C MET* 1.3 75.8 - - - +
153C LYS* 1.3 68.6 + - - +
154C ALA* 3.1 16.1 + - - +
220C PHE* 4.3 2.9 - - - -
230C MET* 3.8 16.4 - - - -
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ARG* 4.8 5.8 - - - +
149C LEU 2.9 12.2 + - - -
150C GLN 4.0 12.3 + - - +
151C MET 3.4 3.7 - - - +
152C SER* 1.3 80.0 - - - +
154C ALA* 1.3 67.4 + - - +
155C LYS* 3.4 10.4 + - - +
176C SER* 3.7 29.6 + - - +
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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