Contacts of the helix formed by residues 171 - 184 (chain C) in PDB entry 2VD0
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 HIS 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C PRO* 4.7 2.6 + - - +
128C MET* 3.6 17.6 - - + +
129C GLN* 3.2 47.2 + - + +
132C ASP* 2.8 28.2 + - - +
167C LEU 3.7 22.0 - - - -
168C LEU* 3.0 14.7 + - + +
170C ASN* 1.3 92.8 + - + +
172C PRO* 1.4 60.5 - - - +
173C ARG 3.2 3.1 - - - -
174C LEU* 2.9 34.0 + - + +
175C VAL* 3.2 12.5 + - - +
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Residues in contact with PRO 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 3.2 12.5 - - - +
45B THR* 3.5 31.2 - - - +
46B LEU 4.6 7.4 - - - +
47B PRO* 5.2 4.7 - - + -
132C ASP* 5.2 1.1 - - - +
168C LEU 4.3 1.1 - - - +
169C ASP 5.0 2.7 - - - +
170C ASN* 3.4 11.0 - - - +
171C HIS* 1.4 88.1 - - - +
173C ARG* 1.3 60.1 + - + +
175C VAL* 3.3 11.3 + - + +
176C THR* 2.8 32.6 + - - -
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Residues in contact with ARG 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU 5.7 0.2 - - - -
44B SER* 3.7 15.7 - - - +
45B THR* 3.8 32.7 - - + +
132C ASP* 2.6 56.5 + - - +
133C THR* 4.1 5.1 + - - +
135C LEU* 3.5 22.4 - - + +
136C GLY* 3.5 35.1 + - - +
137C GLY* 4.4 2.7 - - - +
171C HIS 3.2 1.2 + - - -
172C PRO* 1.3 79.1 - - + +
174C LEU* 1.3 57.4 + - - +
176C THR* 3.6 5.9 + - - -
177C LEU* 3.3 18.5 + - - +
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Residues in contact with LEU 174 (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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128C MET* 3.4 31.4 - - - +
131C LEU* 4.1 12.1 - - + +
132C ASP* 3.9 21.3 - - + +
135C LEU* 3.8 21.5 - - + -
141C LEU* 5.9 1.6 - - + -
153C TRP* 3.4 47.6 + - + +
168C LEU* 3.9 16.8 - - + -
171C HIS* 2.9 21.1 + - + +
173C ARG* 1.3 77.1 - - - +
175C VAL* 1.3 63.8 + - - +
177C LEU* 3.4 5.0 + - + -
178C ARG* 3.2 18.5 + - - +
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Residues in contact with VAL 175 (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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129A GLN* 3.9 27.4 - - + +
130A ASP* 4.6 7.0 - - - +
133A THR* 3.9 16.6 - - + +
168C LEU* 3.6 38.8 - - + +
171C HIS 3.2 8.1 + - - +
172C PRO* 3.3 11.6 + - + +
174C LEU* 1.3 73.7 - - - +
176C THR* 1.3 66.0 + - - +
178C ARG* 3.1 8.8 + - - +
179C LYS* 2.9 40.0 + - + +
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Residues in contact with THR 176 (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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44B SER* 3.2 38.2 + - - -
172C PRO 2.8 26.0 + - - -
173C ARG 3.6 6.7 - - - +
174C LEU 3.3 0.2 - - - -
175C VAL* 1.3 72.9 - - - +
177C LEU* 1.3 56.2 + - - +
179C LYS* 3.2 23.6 + - + +
180C LYS* 2.9 44.1 + - + +
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Residues in contact with LEU 177 (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 LEU* 4.1 18.6 - - + -
139C GLU 3.7 22.0 - - - +
140C TRP* 3.8 16.2 - - + -
141C LEU* 3.7 30.7 - - + -
150C ASP* 3.6 20.9 - - + +
153C TRP* 3.5 26.9 - - + +
173C ARG 3.3 11.7 + - - +
174C LEU* 3.7 10.1 - - + +
175C VAL 3.2 0.4 - - - -
176C THR* 1.3 78.5 - - - +
178C ARG* 1.3 64.2 + - - +
180C LYS* 3.2 5.5 + - + +
181C VAL* 3.0 26.6 + - + +
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Residues in contact with ARG 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 3.8 18.3 + - - +
170A ASN* 5.4 7.7 - - - +
153C TRP* 3.5 19.5 - - + +
154C GLU* 3.0 18.1 + - + +
157C SER* 2.9 26.4 + - - +
158C THR* 3.0 32.7 + - - +
161C LEU* 3.6 23.7 - - - +
168C LEU* 3.5 28.6 - - - +
174C LEU 3.2 5.3 + - - +
175C VAL* 3.1 10.1 + - - +
177C LEU* 1.3 74.1 - - - +
179C LYS* 1.3 57.6 + - - +
181C VAL* 3.3 2.9 + - - +
182C GLN* 2.9 58.3 + - - +
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A HIS* 3.1 59.8 + - + +
129A GLN* 3.5 14.6 - - - +
130A ASP* 2.7 35.4 + - - +
46B LEU 6.0 0.4 + - - -
48B PHE 6.1 0.2 - - - -
49B GLY* 6.3 0.4 - - - -
175C VAL* 2.9 31.9 + - + +
176C THR* 3.3 22.1 + - + +
178C ARG* 1.3 76.6 - - - +
180C LYS* 1.3 56.1 + - + +
182C GLN* 3.4 4.8 + - - -
183C ALA* 3.0 25.3 + - - +
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Residues in contact with LYS 180 (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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40B PRO* 6.3 1.0 - - - +
139C GLU* 3.4 56.2 + - + +
140C TRP* 3.8 24.0 - - + -
176C THR* 2.9 34.1 + - + +
177C LEU* 3.2 8.9 + - - +
179C LYS* 1.3 75.1 - - + +
181C VAL* 1.3 65.2 + - - +
183C ALA* 3.2 15.1 + - - +
184C ILE* 3.4 14.6 + - - +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 4.5 2.7 - - + -
140C TRP* 4.3 7.6 - - + -
146C VAL* 5.0 0.7 - - + -
150C ASP* 3.4 38.1 - - + +
151C PHE* 3.9 25.1 - - + -
154C GLU* 3.8 23.6 - - + -
177C LEU* 3.0 20.3 + - + +
178C ARG 3.7 6.3 - - - +
180C LYS* 1.3 74.9 - - - +
182C GLN* 1.3 62.2 + - - +
183C ALA 3.1 1.4 + - - -
184C ILE* 3.2 25.3 + - - +
187C VAL* 3.5 19.7 - - + +
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Residues in contact with GLN 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR 5.3 1.7 - - - +
122A TYR* 4.8 0.9 - - - -
125A PRO* 5.4 4.6 - - + +
126A HIS* 5.0 5.1 - - + +
129A GLN* 2.9 28.6 + - - +
170A ASN* 5.8 2.4 - - - +
154C GLU* 2.6 34.5 + - - +
158C THR* 4.5 0.2 + - - -
178C ARG* 2.9 52.2 + - - +
179C LYS* 3.9 4.5 - - - +
181C VAL* 1.3 71.6 - - - +
183C ALA* 1.3 56.6 + - - +
184C ILE 3.4 0.7 - - - -
187C VAL* 4.2 7.6 - - - -
188C ALA* 3.3 28.5 - - - +
191C ILE* 3.7 14.8 - - + +
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Residues in contact with ALA 183 (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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122A TYR* 3.3 26.3 - - + -
126A HIS* 3.7 21.5 - - + -
179C LYS 3.0 18.0 + - - +
180C LYS* 3.6 7.4 - - - +
181C VAL 3.1 0.8 - - - -
182C GLN* 1.3 75.4 - - - +
184C ILE* 1.3 64.2 + - - +
185C PRO* 3.1 9.4 - - - +
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Residues in contact with ILE 184 (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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24C TYR* 3.8 28.7 - - + -
140C TRP* 4.4 7.9 - - + -
146C VAL* 3.9 37.0 - - + -
151C PHE* 3.9 15.5 - - + -
180C LYS 3.4 8.3 + - - +
181C VAL* 3.2 19.0 + - - +
183C ALA* 1.3 75.3 - - - +
185C PRO* 1.4 64.4 - - + +
186C ALA* 4.1 7.4 - - + +
187C VAL* 2.9 11.9 + - + +
188C ALA* 2.8 31.7 + - - +
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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