Contacts of the helix formed by residues 147 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ARG 3.3 17.9 + - - +
143A GLY* 4.1 2.9 - - - -
145A LYS 2.8 22.1 - - - +
146A PRO* 1.3 74.4 - - - +
148A PRO* 1.3 71.7 - - + +
149A LEU* 2.9 47.6 + - - +
150A ARG* 3.0 22.7 + - - +
151A GLN* 3.4 19.7 + - - +
20B GLY 4.0 10.8 - - - +
21B ASP* 3.7 18.6 - - - +
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Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASN* 1.3 89.5 - - + +
149A LEU* 1.3 62.7 + - + +
151A GLN* 3.3 18.0 - - + +
152A LYS* 3.1 23.9 + - - +
20B GLY* 4.1 16.4 - - - +
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR 5.5 0.9 - - - +
107A HIS* 4.3 12.3 - - + -
142A ARG* 3.1 43.7 - - + +
147A ASN* 2.9 15.7 + - - +
148A PRO* 1.3 81.6 - - + +
150A ARG* 1.3 64.6 + - - +
151A GLN 3.0 1.6 - - - -
152A LYS* 3.0 35.5 + - + +
153A ASN* 3.1 22.4 + - - +
19B GLN 3.9 24.0 - - - +
20B GLY* 4.8 1.8 - - - -
21B ASP* 3.6 17.7 - - + +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PRO* 3.6 25.6 - - + +
142A ARG* 3.2 37.2 + - - +
143A GLY 3.2 7.7 + - - -
144A GLU 3.1 11.9 + - - -
145A LYS 3.0 25.6 - - - -
146A PRO* 3.3 27.7 - - + +
147A ASN* 3.0 19.4 + - - +
149A LEU* 1.3 75.2 - - - +
151A GLN* 1.3 59.8 - - - +
153A ASN* 4.3 2.4 - - - +
154A ALA* 3.3 22.7 + - - +
180A VAL* 4.3 17.8 - - - +
184A GLY* 3.0 26.9 + - - -
186A ILE* 4.2 4.4 - - - +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO* 5.8 2.8 - - - +
147A ASN* 3.4 22.0 + - - +
148A PRO* 3.3 15.8 - - + +
150A ARG* 1.3 79.6 - - - +
152A LYS* 1.3 66.1 + - - +
154A ALA* 3.3 7.6 - - - +
155A LYS* 3.1 35.1 + - - +
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLY 5.7 2.2 - - - -
106A ASN* 3.0 26.8 + - - -
107A HIS* 3.6 15.0 - - - +
108A GLU 4.6 0.6 - - - +
109A ASN 3.2 22.9 + - - +
110A THR* 5.0 0.9 - - - -
111A ALA* 3.7 25.4 - - + +
114A VAL* 4.5 8.3 - - - -
148A PRO 3.1 13.4 + - - +
149A LEU* 3.0 27.3 + - + +
151A GLN* 1.3 74.6 - - - +
153A ASN* 1.3 72.3 + - - +
155A LYS* 3.0 18.3 + - - +
156A VAL* 3.1 12.0 + - + +
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Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLY 5.1 0.5 - - - +
104A THR* 3.3 28.1 + - - +
139A LEU* 3.7 37.8 - - + +
140A LEU 3.1 25.3 + - - +
141A PRO* 5.0 1.7 - - + +
142A ARG* 3.9 12.7 - - - +
149A LEU* 3.1 14.2 + - - +
150A ARG* 4.4 3.1 - - - +
152A LYS* 1.3 83.2 - - - +
154A ALA* 1.3 64.9 + - - +
156A VAL* 3.1 5.5 + - - +
157A ASN* 2.9 27.2 + - - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG 3.3 15.0 + - - +
151A GLN* 3.3 12.3 - - - +
152A LYS 3.1 0.6 - - - -
153A ASN* 1.3 78.8 - - - +
155A LYS* 1.3 63.4 + - - +
157A ASN* 3.1 11.3 + - - +
158A GLN* 3.0 20.8 + - - +
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.8 15.3 - - + +
112A GLU* 4.7 15.3 - - - +
151A GLN* 3.1 23.0 + - - +
152A LYS* 3.0 10.5 + - - +
154A ALA* 1.3 73.5 - - - +
156A VAL* 1.3 68.6 + - - +
158A GLN* 2.8 40.4 - - + +
159A LEU* 2.9 28.2 + - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.7 30.7 - - + +
114A VAL* 4.0 15.0 - - + -
115A ALA* 4.4 6.7 - - - -
118A ILE* 3.9 11.7 - - + -
139A LEU* 3.8 26.2 - - + -
152A LYS* 3.1 14.5 + - + +
153A ASN* 3.1 9.3 + - - +
155A LYS* 1.3 74.0 - - - +
157A ASN* 1.3 65.0 + - - +
159A LEU* 3.1 5.7 + - - +
160A LEU* 2.9 47.6 + - + +
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Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY* 3.2 10.2 - - - -
139A LEU* 2.9 48.3 + - - +
153A ASN 2.9 16.8 + - - +
154A ALA* 3.3 12.1 - - - +
156A VAL* 1.3 77.9 - - - +
158A GLN* 1.3 51.1 + - - +
160A LEU* 3.2 8.2 + - - +
161A LYS* 2.9 35.4 + - - +
172A LEU* 4.2 6.2 - - + +
174A ASP* 3.4 33.3 + - - +
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Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA 3.0 9.8 + - - +
155A LYS* 2.8 37.6 - - + +
157A ASN* 1.3 73.5 - - - +
159A LEU* 1.3 68.1 + - + +
161A LYS* 3.2 19.0 + - - +
162A VAL* 3.4 11.6 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 4.4 1.8 - - - +
112A GLU* 3.7 43.3 - - + +
115A ALA* 3.8 18.6 - - + -
119A GLU* 5.0 1.8 - - - +
155A LYS* 2.9 28.9 + - + +
156A VAL 3.6 5.6 - - - +
158A GLN* 1.3 84.8 - - + +
160A LEU* 1.3 59.1 + - - +
162A VAL* 3.3 11.1 + - + +
163A SER* 2.9 30.9 + - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA* 4.1 17.3 - - + +
118A ILE* 3.5 37.0 - - + -
119A GLU* 3.9 23.1 - - + +
136A VAL* 4.4 13.2 - - + -
138A GLY* 5.8 1.6 - - - -
139A LEU* 5.8 0.9 - - + -
156A VAL* 2.9 28.3 + - + +
157A ASN* 3.6 8.1 - - - +
159A LEU* 1.3 73.3 - - - +
161A LYS* 1.3 66.2 + - - +
162A VAL 3.0 1.8 - - - -
163A SER* 4.1 3.4 - - - +
164A LEU* 2.9 45.4 + - + +
172A LEU* 3.9 17.0 - - + -
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASN 2.9 13.4 + - - +
158A GLN* 3.4 12.8 - - - +
160A LEU* 1.3 75.1 - - - +
162A VAL* 1.3 59.8 + - + +
165A PRO* 3.0 23.2 - - - +
172A LEU* 3.8 25.4 - - + +
174A ASP* 6.0 0.4 - - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLN 3.4 6.8 + - - +
159A LEU* 3.3 15.1 + - + +
160A LEU 3.0 0.6 - - - -
161A LYS* 1.3 83.7 - - + +
163A SER* 1.3 65.3 + - - +
165A PRO* 3.2 17.5 - - - +
166A LYS* 3.8 22.8 - - - +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 2.6 43.5 + - - +
159A LEU* 2.9 15.2 + - - -
160A LEU* 4.1 1.9 + - - +
162A VAL* 1.3 81.9 - - - +
164A LEU* 1.3 65.7 + - - +
165A PRO* 3.5 0.2 - - - -
166A LYS* 3.0 30.8 - - - +
167A LEU* 4.5 9.0 - - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 5.6 0.9 - - + -
119A GLU* 4.9 5.6 - - + -
122A VAL* 4.0 26.5 - - + -
136A VAL* 4.1 19.7 - - + -
160A LEU* 2.9 34.2 + - + +
163A SER* 1.3 80.5 + - - +
165A PRO* 1.3 58.8 - - + +
166A LYS 2.2 27.3 - - - +
167A LEU* 3.7 12.4 - - + +
170A VAL* 3.6 38.6 - - + +
171A GLN* 4.8 1.1 - - - -
172A LEU* 4.0 29.4 - - + +
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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