Contacts of the helix formed by residues 147 - 164 (chain R) in PDB entry 1VYH
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 147 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20Q GLY 4.0 10.3 - - - +
21Q ASP* 3.7 30.5 - - - +
142R ARG 3.8 14.1 + - - +
143R GLY* 4.0 1.4 - - - -
145R LYS 2.6 21.3 - - - +
146R PRO* 1.3 74.6 - - - +
148R PRO* 1.3 74.3 - - + +
149R LEU* 2.8 31.5 + - - +
150R ARG* 3.0 24.4 + - - +
151R GLN* 3.4 20.3 + - - +
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Residues in contact with PRO 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q GLY* 4.6 12.8 - - - +
147R ASN* 1.3 88.0 - - + +
149R LEU* 1.3 63.0 + - + +
151R GLN* 3.5 14.5 + - + +
152R LYS* 3.0 25.3 + - - +
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Residues in contact with LEU 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q GLN 4.0 20.6 - - - +
20Q GLY* 5.0 2.0 - - - -
21Q ASP* 4.0 14.8 - - + +
107R HIS* 4.0 19.7 - - + -
142R ARG* 3.2 50.9 - - - +
147R ASN* 2.8 15.8 + - - +
148R PRO* 1.3 78.8 - - + +
150R ARG* 1.3 68.2 + - - +
151R GLN 3.0 1.6 - - - -
152R LYS* 2.9 36.2 + - + +
153R ASN* 3.0 19.8 + - - +
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Residues in contact with ARG 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R PRO* 3.9 20.8 - - + +
142R ARG* 3.3 36.6 + - - +
143R GLY 3.0 11.1 + - - -
144R GLU 2.7 33.1 + - - -
145R LYS 3.2 3.8 + - - -
146R PRO* 3.5 26.7 - - + +
147R ASN* 3.0 16.4 + - - +
149R LEU* 1.3 76.5 - - - +
151R GLN* 1.3 60.6 + - - +
153R ASN* 4.3 2.5 - - - +
154R ALA* 3.3 22.5 + - - +
180R VAL* 3.1 24.2 - - - +
184R GLY* 2.6 26.8 + - - -
186R ILE* 3.8 8.2 - - - +
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Residues in contact with GLN 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R PRO* 5.8 2.6 - - - +
147R ASN* 3.4 27.9 + - - +
148R PRO* 3.5 12.2 - - + +
149R LEU 3.0 0.6 - - - -
150R ARG* 1.3 79.6 - - - +
152R LYS* 1.3 63.5 + - - +
154R ALA* 3.3 8.1 - - + +
155R LYS* 3.1 28.3 + - - +
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Residues in contact with LYS 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R GLY 5.6 2.2 - - - -
106R ASN 3.7 19.9 + - - -
107R HIS* 4.0 11.8 - - - +
108R GLU 4.5 1.2 - - - +
109R ASN 2.8 29.7 + - - +
110R THR* 4.9 1.1 - - - +
111R ALA* 3.7 24.1 - - - +
114R VAL* 4.6 6.5 - - + -
139R LEU* 5.9 0.2 - - + -
148R PRO 3.0 14.7 + - - +
149R LEU* 2.9 29.3 + - + +
151R GLN* 1.3 74.6 - - - +
153R ASN* 1.3 75.4 + - - +
155R LYS* 3.0 19.0 + - - +
156R VAL* 3.0 19.2 + - + +
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Residues in contact with ASN 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R GLY 5.0 0.2 - - - +
104R THR* 3.6 25.3 + - - +
139R LEU* 3.3 38.6 - - + +
140R LEU 2.7 30.3 + - - +
141R PRO* 5.4 0.2 - - + -
142R ARG* 4.0 8.6 - - - +
149R LEU* 3.0 15.5 + - - +
150R ARG* 4.3 4.7 - - - +
152R LYS* 1.3 84.9 - - - +
154R ALA* 1.3 63.2 + - - +
156R VAL* 3.1 10.7 + - - +
157R ASN* 3.0 26.1 + - - +
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Residues in contact with ALA 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150R ARG 3.3 14.7 + - - +
151R GLN* 3.3 13.0 - - - +
152R LYS 3.2 0.6 - - - -
153R ASN* 1.3 77.2 - - - +
155R LYS* 1.3 63.3 + - - +
157R ASN* 3.1 13.2 + - - +
158R GLN* 3.0 20.9 + - - +
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Residues in contact with LYS 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R ALA* 3.7 16.9 - - + +
112R GLU* 3.4 26.1 + - - +
151R GLN* 3.1 17.5 + - - +
152R LYS* 3.0 11.1 + - - +
154R ALA* 1.3 74.5 - - - +
156R VAL* 1.3 64.6 + - - +
158R GLN* 2.9 23.3 + - + +
159R LEU* 2.9 24.5 + - + +
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Residues in contact with VAL 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R ALA* 3.9 26.0 - - + +
114R VAL* 3.7 29.4 - - + -
115R ALA* 4.1 11.4 - - - +
118R ILE* 3.9 17.9 - - + -
139R LEU* 4.2 14.8 - - + -
152R LYS* 3.0 22.1 + - + +
153R ASN* 3.1 10.1 + - - +
155R LYS* 1.3 75.3 - - - +
157R ASN* 1.3 63.3 + - - +
159R LEU* 3.2 2.8 + - - +
160R LEU* 2.9 35.1 + - + +
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Residues in contact with ASN 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138R GLY* 3.2 11.2 - - - -
139R LEU* 2.9 44.7 + - - +
153R ASN 3.0 12.0 + - - +
154R ALA* 3.3 13.9 - - - +
156R VAL* 1.3 75.8 - - - +
158R GLN* 1.3 64.1 + - - +
160R LEU* 3.2 9.3 + - - +
161R LYS* 2.9 24.4 + - - +
172R LEU* 4.4 8.0 - - + +
174R ASP* 3.3 38.2 + - - +
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Residues in contact with GLN 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R ALA 3.0 11.5 + - - +
155R LYS* 2.9 19.3 + - + +
157R ASN* 1.3 78.2 - - - +
159R LEU* 1.3 70.0 + - + +
161R LYS* 3.1 25.7 + - - +
162R VAL* 3.3 17.3 + - + +
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Residues in contact with LEU 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111R ALA 4.8 2.0 - - - -
112R GLU* 3.9 46.4 - - + +
115R ALA* 4.1 15.9 - - + -
119R GLU* 5.6 0.7 - - - +
155R LYS* 2.9 27.6 + - + +
156R VAL 3.9 3.1 - - - +
158R GLN* 1.3 79.9 - - + +
160R LEU* 1.3 57.5 + - - +
162R VAL* 3.3 11.5 + - + +
163R SER* 2.8 33.4 + - - +
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Residues in contact with LEU 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R ALA* 4.0 24.9 - - + +
118R ILE* 3.9 38.6 - - + -
119R GLU* 4.4 2.5 - - + -
136R VAL* 4.4 13.2 - - + -
137R LEU 5.9 0.4 - - - +
138R GLY* 5.9 1.1 - - - -
139R LEU* 6.3 0.7 - - + -
156R VAL* 2.9 27.4 + - + +
157R ASN* 3.7 7.4 - - - +
159R LEU* 1.3 75.0 - - - +
161R LYS* 1.3 67.2 + - - +
162R VAL 3.1 1.6 - - - -
163R SER* 3.8 10.1 - - - +
164R LEU* 2.9 57.4 + - + +
172R LEU* 4.3 11.7 - - + -
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Residues in contact with LYS 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157R ASN 2.9 12.6 + - - +
158R GLN* 3.1 22.0 + - - +
160R LEU* 1.3 75.6 - - - +
162R VAL* 1.3 57.6 + - + +
165R PRO* 3.1 23.0 - - - +
172R LEU* 3.9 22.7 - - + +
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Residues in contact with VAL 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158R GLN* 3.3 12.1 + - + +
159R LEU* 3.3 16.0 + - + +
160R LEU 3.1 0.4 - - - -
161R LYS* 1.3 81.2 - - + +
163R SER* 1.3 63.9 + - - +
164R LEU 3.5 0.2 - - - -
165R PRO* 3.3 16.9 - - - +
166R LYS* 4.5 18.1 + - - +
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Residues in contact with SER 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R GLU* 3.2 35.3 + - - +
159R LEU 2.8 28.2 + - - -
160R LEU* 3.8 5.7 - - - +
162R VAL* 1.3 77.2 - - - +
164R LEU* 1.3 62.7 + - - +
165R PRO* 3.6 0.2 - - - -
166R LYS* 3.8 24.3 + - - +
167R LEU* 4.4 12.3 - - - +
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Residues in contact with LEU 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118R ILE* 5.0 1.6 - - + -
119R GLU* 4.9 8.3 - - + -
122R VAL* 4.1 30.7 - - + -
136R VAL* 4.2 19.1 - - + -
160R LEU* 2.9 47.4 + - + +
161R LYS* 5.5 0.2 - - - -
163R SER* 1.3 75.9 - - - +
165R PRO* 1.3 56.4 - - + +
166R LYS 2.3 25.9 - - - +
167R LEU* 3.6 8.0 - - + +
170R VAL* 3.8 27.9 - - + +
171R GLN* 4.7 1.6 - - - -
172R LEU* 3.7 33.2 - - + +
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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
------------------------------------------------------------
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