Contacts of the helix formed by residues 147 - 164 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY 4.1 11.0 - - - +
21E ASP* 3.6 23.1 - - - +
142F ARG 3.2 18.9 + - - +
143F GLY* 4.1 1.9 - - - -
145F LYS 2.8 21.0 - - - +
146F PRO* 1.3 76.0 - - - +
148F PRO* 1.3 66.1 - - + +
149F LEU* 2.7 49.7 + - - +
150F ARG* 3.0 25.2 + - - +
151F GLN* 3.5 11.9 + - - +
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Residues in contact with PRO 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY* 4.2 14.6 - - - +
147F ASN* 1.3 86.2 - - + +
149F LEU* 1.3 64.5 + - + +
151F GLN* 3.2 19.3 - - + +
152F LYS* 3.0 23.4 + - - +
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Residues in contact with LEU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E GLN* 3.3 29.8 - - + +
20E GLY* 4.1 0.7 - - - -
21E ASP* 3.7 34.1 - - + +
107F HIS* 4.5 14.4 - - + -
142F ARG* 4.3 23.3 - - + +
147F ASN* 2.7 13.7 + - - +
148F PRO* 1.3 79.8 - - + +
150F ARG* 1.3 64.8 + - - +
151F GLN 3.0 1.6 - - - -
152F LYS* 3.0 35.9 + - + +
153F ASN* 3.1 24.8 + - - +
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Residues in contact with ARG 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PRO* 3.9 21.1 - - + +
142F ARG* 3.1 36.7 + - - +
143F GLY 2.9 12.1 + - - -
144F GLU 2.8 31.5 + - - -
145F LYS 3.3 4.2 - - - -
146F PRO* 3.3 26.1 - - + +
147F ASN* 3.0 18.7 + - - +
149F LEU* 1.3 76.5 - - - +
151F GLN* 1.3 60.9 + - - +
153F ASN* 4.4 2.3 - - - +
154F ALA* 3.2 23.6 + - - +
180F VAL* 3.5 15.4 - - - +
184F GLY* 2.8 24.0 + - - -
186F ILE* 3.6 15.9 - - - +
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Residues in contact with GLN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C HIS* 3.3 32.2 + - - +
190C GLY* 4.0 10.6 + - - +
217C LYS* 6.2 1.3 - - - -
226C CYS* 6.1 4.9 - - + -
147F ASN 3.5 5.8 + - - +
148F PRO* 3.2 23.5 - - - +
150F ARG* 1.3 76.6 - - - +
152F LYS* 1.3 65.2 + - - +
154F ALA* 3.3 8.4 + - - +
155F LYS* 3.0 41.0 + - - +
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLY 5.5 2.9 - - - -
106F ASN* 2.9 23.8 + - - -
107F HIS* 3.7 14.7 - - - +
108F GLU 4.3 0.8 - - - +
109F ASN 2.7 29.5 + - - +
110F THR* 4.8 1.6 - - - -
111F ALA* 4.0 24.7 - - + +
114F VAL* 4.9 7.9 - - - -
148F PRO 3.0 12.8 + - - +
149F LEU* 3.0 26.3 + - + +
151F GLN* 1.3 74.9 - - - +
153F ASN* 1.3 75.2 + - - +
155F LYS* 3.0 12.2 + - - +
156F VAL* 3.0 22.4 + - + +
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Residues in contact with ASN 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLY 5.1 0.7 - - - +
104F THR* 3.7 21.4 + - - +
139F LEU* 3.4 33.9 - - + +
140F LEU 3.0 25.8 + - - +
141F PRO* 4.9 1.2 - - + +
142F ARG* 3.8 12.7 - - - +
149F LEU* 3.1 17.4 + - - +
150F ARG* 4.5 2.0 - - - +
152F LYS* 1.3 85.2 - - - +
154F ALA* 1.3 64.4 + - - +
156F VAL* 3.0 11.3 + - - +
157F ASN* 2.9 27.6 + - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TYR* 3.3 40.2 - - + -
226C CYS 5.8 0.9 - - - +
150F ARG 3.2 17.4 + - - +
151F GLN* 3.3 12.6 - - - +
152F LYS 3.2 0.8 - - - -
153F ASN* 1.3 76.4 - - - +
155F LYS* 1.3 63.4 + - - +
157F ASN* 3.1 5.8 + - - +
158F GLN* 3.0 25.0 + - - -
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Residues in contact with LYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C LYS* 6.0 1.4 - - - +
226C CYS* 5.4 14.0 + - - +
111F ALA* 3.6 20.9 - - + -
112F GLU* 4.3 17.3 - - - +
151F GLN* 3.0 32.6 + - - +
152F LYS* 3.0 11.5 + - - +
154F ALA* 1.3 73.6 - - - +
156F VAL* 1.3 66.0 + - - +
158F GLN* 2.7 35.4 - - + +
159F LEU* 3.0 18.5 + - + +
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Residues in contact with VAL 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ALA* 3.6 21.1 - - - +
114F VAL* 3.6 33.2 - - + -
115F ALA* 4.5 4.7 - - + -
118F ILE* 4.4 3.8 - - + -
139F LEU* 4.3 17.7 - - + -
152F LYS* 3.0 19.3 + - + +
153F ASN* 3.0 14.8 + - - +
155F LYS* 1.3 75.2 - - - +
157F ASN* 1.3 66.8 + - - +
159F LEU* 3.2 8.3 + - - +
160F LEU* 2.9 42.2 + - + +
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Residues in contact with ASN 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TYR* 2.6 31.2 + - + +
138F GLY* 3.5 8.6 - - - -
139F LEU* 2.9 43.9 + - - +
153F ASN 2.9 15.2 + - - +
154F ALA* 3.1 9.1 + - - +
156F VAL* 1.3 79.0 - - - +
158F GLN* 1.3 62.4 - - - +
160F LEU* 3.0 9.1 + - - +
161F LYS* 2.9 24.5 + - - +
172F LEU* 3.9 5.9 - - + +
174F ASP* 2.6 24.7 + - - +
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Residues in contact with GLN 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C GLU* 4.7 2.4 + - - -
225C TYR* 2.9 37.3 - - - +
226C CYS 2.6 29.1 - - - +
227C VAL* 3.1 29.6 - - + +
154F ALA 3.0 10.7 + - - -
155F LYS* 2.7 25.3 + - + +
157F ASN* 1.3 72.4 - - - +
159F LEU* 1.3 75.3 + - + +
161F LYS* 3.1 15.6 + - - +
162F VAL* 3.3 17.0 + - + +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ALA 4.5 2.0 - - - +
112F GLU* 3.7 44.4 - - + +
115F ALA* 3.9 17.3 - - + -
119F GLU* 5.2 1.3 - - - +
155F LYS* 3.3 20.2 - - + +
156F VAL 3.6 6.3 - - - +
158F GLN* 1.3 90.3 - - + +
160F LEU* 1.3 57.6 + - - +
162F VAL* 3.3 9.0 + - + +
163F SER* 2.9 32.3 + - - -
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ALA* 4.1 17.0 - - + +
118F ILE* 3.8 37.9 - - + -
119F GLU* 3.9 15.3 - - + +
136F VAL* 3.9 18.4 - - + -
137F LEU 5.6 0.9 - - - +
138F GLY* 5.8 0.4 - - - -
139F LEU* 5.7 1.3 - - + -
156F VAL* 2.9 27.4 + - + +
157F ASN* 3.5 7.9 - - - +
159F LEU* 1.3 73.1 - - - +
161F LYS* 1.3 65.5 + - - +
162F VAL 3.0 1.8 - - - -
163F SER* 3.9 13.2 - - - +
164F LEU* 2.9 42.2 + - + +
172F LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLU* 3.2 30.7 + - - -
222C GLN* 5.9 1.2 + - - -
223C THR* 5.8 3.4 - - - +
157F ASN 2.9 12.8 + - - +
158F GLN* 3.4 11.4 - - - +
160F LEU* 1.3 73.7 - - - +
162F VAL* 1.3 59.4 + - + +
165F PRO* 3.0 25.9 - - - +
172F LEU* 3.6 19.9 - - + +
174F ASP* 6.5 0.7 - - + -
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Residues in contact with VAL 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F GLN* 3.3 14.7 + - + +
159F LEU* 3.5 10.5 - - + +
160F LEU 3.0 0.8 - - - -
161F LYS* 1.3 81.4 - - + +
163F SER* 1.3 63.8 + - - +
165F PRO* 3.5 9.7 - - - +
166F LYS* 3.8 26.6 + - - +
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Residues in contact with SER 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F GLU* 2.5 40.9 + - - +
159F LEU 2.9 15.0 + - - -
160F LEU* 3.1 7.3 + - - +
162F VAL* 1.3 78.5 - - - +
164F LEU* 1.3 59.9 + - - +
165F PRO 3.6 0.4 - - - -
166F LYS* 3.3 21.9 - - - +
167F LEU* 3.0 25.1 - - - +
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ILE* 5.4 0.4 - - + -
119F GLU* 4.8 4.9 - - + -
122F VAL* 4.2 19.7 - - + -
136F VAL* 4.2 18.6 - - + -
160F LEU* 2.9 37.3 + - + +
163F SER* 1.3 77.6 + - - +
165F PRO* 1.3 57.3 - - + +
166F LYS 2.2 26.7 - - - +
167F LEU* 3.6 15.8 - - + +
170F VAL* 3.9 34.8 - - + +
171F GLN* 4.3 2.5 - - - -
172F LEU* 3.8 38.8 - - + +
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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