Contacts of the helix formed by residues 155 - 170 (chain A) in PDB entry 1VLP
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A TYR 3.2 1.4 + - - -
154A GLU* 1.3 83.6 + - - +
156A GLN* 1.3 59.5 + - - +
157A LEU 3.3 2.5 - - - -
158A GLU* 3.3 28.7 + - + +
159A GLN* 2.9 32.9 + - + +
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Residues in contact with GLN 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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152A ASP 4.7 0.6 + - - -
153A TYR* 3.1 27.7 + - + +
154A GLU 3.2 7.1 + - - -
155A ASN* 1.3 73.6 - - - +
157A LEU* 1.3 68.5 + - - +
158A GLU* 4.1 0.2 + - - -
159A GLN* 3.4 14.5 + - - +
160A ALA* 3.1 24.6 + - - +
187A ALA* 5.2 2.6 - - + +
190A LEU* 4.2 17.5 - - + -
191A ILE* 3.9 22.9 - - + +
357A PHE 4.6 3.5 - - - +
360A ASP 3.0 27.0 + - - +
361A PHE* 3.3 47.5 - - + +
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Residues in contact with LEU 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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153A TYR 4.9 0.2 + - - -
155A ASN 3.3 0.4 - - - -
156A GLN* 1.3 82.0 - - - +
158A GLU* 1.3 77.5 + - + +
160A ALA* 3.3 0.7 + - - +
161A GLU* 2.9 26.9 + - - +
190A LEU* 3.8 27.5 - - + +
193A GLN* 3.6 31.9 - - + +
194A GLY* 3.4 26.9 - - - +
197A LYS* 4.2 23.8 - - + -
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Residues in contact with GLU 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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155A ASN* 3.3 40.1 + - + +
156A GLN 3.4 0.2 - - - -
157A LEU* 1.3 91.9 + - + +
159A GLN* 1.3 56.7 + - - +
161A GLU* 3.4 15.5 + - - +
162A LYS* 3.0 29.3 + - - +
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Residues in contact with GLN 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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155A ASN* 2.9 20.4 + - + +
156A GLN* 3.8 17.2 + - - +
157A LEU 3.3 0.2 - - - -
158A GLU* 1.3 73.3 - - - +
160A ALA* 1.3 65.6 + - - +
162A LYS* 3.5 6.9 + - - +
163A LYS* 3.1 42.1 + - - +
191A ILE* 6.3 0.2 - - - +
357A PHE 5.7 1.0 + - - -
360A ASP* 2.9 50.4 + - - +
362A ARG* 6.1 1.2 - - - +
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Residues in contact with ALA 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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156A GLN 3.1 13.6 + - - +
157A LEU 3.7 4.0 - - - +
159A GLN* 1.3 75.0 - - - +
161A GLU* 1.3 60.8 + - - +
163A LYS* 3.2 6.0 + - - +
164A ALA* 2.9 30.1 + - - +
191A ILE* 3.6 46.0 - - + +
194A GLY* 4.3 2.7 - - - -
195A ILE* 4.5 0.6 - - - +
357A PHE* 3.9 20.0 - - + +
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Residues in contact with GLU 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 LEU* 2.9 17.4 + - + +
158A GLU* 3.5 18.1 - - - +
159A GLN 3.3 0.2 - - - -
160A ALA* 1.3 76.9 - - - +
162A LYS* 1.3 56.6 + - - +
164A ALA* 3.3 2.8 + - - +
165A GLU* 2.9 59.1 + - - +
194A GLY* 3.3 26.6 - - - +
197A LYS* 3.3 44.2 - - - +
198A ALA* 3.9 6.1 - - - +
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Residues in contact with LYS 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 GLU 3.0 17.6 + - - +
159A GLN* 3.8 6.7 - - - +
160A ALA 3.3 0.2 - - - -
161A GLU* 1.3 75.4 - - - +
163A LYS* 1.3 64.8 + - + +
165A GLU* 3.3 9.6 + - - +
166A THR* 3.0 34.3 + - - +
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Residues in contact with LYS 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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159A GLN* 3.1 32.3 + - - +
160A ALA* 3.2 6.6 + - - +
162A LYS* 1.3 75.5 - - + +
164A ALA* 1.3 62.8 + - - +
166A THR* 3.1 5.9 + - - -
167A LEU* 3.0 28.5 + - - +
332A VAL* 3.7 23.2 - - + +
356A ASN* 2.7 46.5 + - - +
357A PHE* 4.0 25.5 + - + +
360A ASP* 2.8 26.9 + - - +
109B GLU* 5.6 5.4 - - - -
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Residues in contact with ALA 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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160A ALA 2.9 15.7 + - - +
161A GLU 3.3 0.2 + - - -
163A LYS* 1.3 76.5 - - - +
165A GLU* 1.3 56.9 + - - +
167A LEU* 3.2 13.8 + - - +
168A PHE* 2.9 43.2 + - + -
174A PHE* 4.2 11.4 - - + -
195A ILE* 4.1 16.6 - - + -
198A ALA* 3.5 22.4 - - + -
357A PHE* 4.7 1.1 - - + -
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Residues in contact with GLU 165 (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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161A GLU* 2.9 50.4 + - - +
162A LYS* 3.7 8.2 - - - +
163A LYS 3.2 0.2 - - - -
164A ALA* 1.3 76.5 - - - +
166A THR* 1.3 63.0 + - - +
168A PHE* 3.4 6.6 + - + +
169A ASP* 3.0 33.6 + - - +
197A LYS 4.9 0.5 - - - +
198A ALA* 3.6 21.3 - - + +
201A GLY* 5.8 2.4 - - - -
205A ARG* 4.6 0.6 + - - +
206A ASN* 6.0 0.7 - - - +
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Residues in contact with THR 166 (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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162A LYS* 3.0 22.8 + - - +
163A LYS* 3.6 8.3 - - - -
165A GLU* 1.3 77.0 - - - +
167A LEU* 1.3 62.3 + - - +
169A ASP* 3.3 9.3 + - - +
170A ASN* 2.9 41.9 + - - +
332A VAL* 3.6 23.8 - - + -
336A ILE* 4.0 5.2 - - + -
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Residues in contact with LEU 167 (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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163A LYS 3.0 21.7 + - - +
164A ALA 3.5 5.2 - - - +
166A THR* 1.3 76.3 - - - +
168A PHE* 1.3 62.7 + - - +
170A ASN* 3.0 11.8 + - - -
172A ILE* 3.1 48.6 + - + +
174A PHE* 3.7 35.9 - - + -
332A VAL* 4.0 25.8 - - + +
335A ALA* 4.0 20.4 - - + -
336A ILE* 5.1 0.9 - - + -
353A ILE* 3.7 24.5 - - + -
357A PHE* 4.2 6.1 - - + -
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Residues in contact with PHE 168 (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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164A ALA* 2.9 24.4 + - + +
165A GLU* 3.8 7.2 - - - +
167A LEU* 1.3 75.5 - - - +
169A ASP* 1.3 57.6 + - - +
171A GLY* 2.9 16.6 + - - -
172A ILE 4.4 0.2 - - - -
174A PHE* 3.4 33.2 - + - -
195A ILE* 4.9 0.9 - - + -
198A ALA* 3.9 10.1 - - + -
199A VAL* 3.6 43.3 - - + -
205A ARG* 3.5 14.9 + - - +
206A ASN* 3.4 41.1 - - + +
209A LEU* 3.5 43.2 - - + +
210A LEU* 3.8 7.9 - - + -
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Residues in contact with ASP 169 (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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165A GLU* 3.0 20.5 + - - +
166A THR* 3.3 11.1 + - - +
168A PHE* 1.3 76.1 - - - +
170A ASN* 1.3 63.9 + - - +
171A GLY 3.3 0.8 + - - -
205A ARG* 2.9 31.8 + - - +
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Residues in contact with ASN 170 (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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166A THR* 2.9 26.8 + - - +
167A LEU 3.0 8.3 + - - +
169A ASP* 1.3 82.6 - - - +
171A GLY* 1.3 62.4 + - - +
172A ILE* 3.2 23.0 + - + +
336A ILE* 3.5 36.2 - - + +
339A SER* 5.2 0.5 + - - -
340A HIS* 5.1 4.3 + - - -
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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