Contacts of the helix formed by residues 155 - 170 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D TYR 3.3 1.4 + - - -
154D GLU* 1.3 87.3 + - - +
156D GLN* 1.3 59.6 + - - +
157D LEU 3.4 2.2 - - - -
158D GLU* 3.3 25.9 + - + +
159D GLN* 2.8 33.0 + - + +
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Residues in contact with GLN 156 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ASP 4.8 0.4 + - - -
153D TYR* 3.2 25.6 + - + +
154D GLU 3.2 7.1 + - - -
155D ASN* 1.3 76.6 - - - +
157D LEU* 1.3 66.7 + - - +
158D GLU* 4.0 0.2 + - - -
159D GLN* 3.7 13.8 + - - +
160D ALA* 3.1 23.7 + - - +
187D ALA* 5.2 2.6 - - + +
190D LEU* 4.3 17.5 - - + -
191D ILE* 3.9 23.0 - - + +
357D PHE 4.7 3.6 - - - +
358D THR 5.6 0.3 - - - -
360D ASP 3.0 26.5 + - - +
361D PHE* 3.4 49.1 - - + +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASN 3.4 0.6 - - - -
156D GLN* 1.3 77.1 - - - +
158D GLU* 1.3 73.8 + - - +
160D ALA* 3.3 2.3 + - - -
161D GLU* 2.8 44.9 + - - +
190D LEU* 3.8 27.2 + - + +
193D GLN* 3.4 36.8 - - + +
194D GLY* 3.4 21.7 - - - +
197D LYS* 4.2 22.0 - - + +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASN* 3.3 35.1 + - + +
156D GLN 3.3 0.2 - - - -
157D LEU* 1.3 89.8 + - + +
159D GLN* 1.3 59.6 + - - +
161D GLU* 3.6 11.0 - - - +
162D LYS* 2.9 31.4 + - - +
197D LYS* 5.9 2.1 + - - +
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASN* 2.8 24.8 + - + +
156D GLN* 3.7 17.3 + - - +
158D GLU* 1.3 74.3 - - - +
160D ALA* 1.3 62.1 + - - +
162D LYS* 3.4 6.1 + - - +
163D LYS* 3.2 41.9 + - - +
191D ILE* 6.2 0.6 - - - +
357D PHE 5.6 1.0 + - - -
360D ASP* 2.8 52.6 + - - +
362D ARG* 5.9 2.6 - - - +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D GLN 3.1 14.1 + - - +
157D LEU 3.6 3.8 - - - +
159D GLN* 1.3 75.1 - - - +
161D GLU* 1.3 66.6 + - - +
163D LYS* 3.3 6.9 + - - +
164D ALA* 3.1 23.2 + - - +
191D ILE* 3.5 46.9 - - + +
194D GLY* 4.3 2.5 - - - -
195D ILE* 4.6 0.3 - - - +
357D PHE* 3.9 17.6 - - + -
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Residues in contact with GLU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 2.8 25.1 + - - +
158D GLU* 3.6 10.5 - - - +
160D ALA* 1.3 78.5 - - - +
162D LYS* 1.3 56.6 + - - +
164D ALA* 3.3 2.4 + - - +
165D GLU* 2.9 31.4 + - + +
194D GLY* 3.3 22.6 - - - +
197D LYS* 2.8 42.8 + - - +
198D ALA* 3.7 15.5 + - + +
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLU 2.9 17.6 + - - +
159D GLN* 3.7 6.7 - - - +
161D GLU* 1.3 77.7 - - - +
163D LYS* 1.3 63.8 + - + +
165D GLU* 3.4 20.1 + - - +
166D THR* 3.0 40.5 + - - +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLN* 3.2 30.4 + - + +
160D ALA* 3.3 7.5 + - - +
162D LYS* 1.3 76.7 - - + +
164D ALA* 1.3 64.0 - - - +
166D THR* 3.2 5.5 + - - -
167D LEU* 3.0 28.9 + - - +
332D VAL* 3.7 23.9 - - + +
356D ASN* 2.6 47.4 + - - +
357D PHE* 4.0 26.4 + - + +
360D ASP* 2.7 28.4 + - - +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ALA 3.1 13.4 + - - +
161D GLU 3.7 2.9 - - - +
163D LYS* 1.3 78.6 - - - +
165D GLU* 1.3 52.6 + - - +
167D LEU* 3.1 4.5 + - - +
168D PHE* 2.8 46.8 + - + -
174D PHE* 4.1 23.8 - - + -
195D ILE* 4.2 15.5 - - + -
198D ALA* 3.6 20.9 - - + -
357D PHE* 4.7 1.3 - - + -
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D GLU* 2.9 22.1 + - + +
162D LYS* 3.7 24.7 + - - +
164D ALA* 1.3 72.2 - - - +
166D THR* 1.3 57.3 + - - +
168D PHE* 3.3 10.3 + - + +
169D ASP* 2.9 55.1 + - - +
198D ALA* 3.9 10.6 - - + +
205D ARG* 5.5 3.8 - - - +
206D ASN* 6.4 0.2 - - - +
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Residues in contact with THR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LYS* 3.0 37.1 + - - +
163D LYS* 3.6 5.8 - - - -
165D GLU* 1.3 75.1 + - - +
167D LEU* 1.3 62.5 + - - +
169D ASP* 3.3 7.1 + - - +
170D ASN* 2.8 41.5 + - - +
332D VAL* 3.6 24.0 - - + -
336D ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS 3.0 22.8 + - - +
164D ALA 3.1 4.2 + - - +
166D THR* 1.3 75.8 - - - +
168D PHE* 1.3 64.8 + - - +
170D ASN* 3.1 10.6 + - - -
172D ILE* 3.0 45.2 + - + +
174D PHE* 3.8 34.8 - - + -
332D VAL* 4.1 23.3 - - + -
335D ALA* 3.7 30.1 - - + -
353D ILE* 3.6 24.7 - - + -
357D PHE* 4.6 3.6 - - + -
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Residues in contact with PHE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA* 2.8 26.8 + - + +
165D GLU* 3.6 5.8 - - + +
167D LEU* 1.3 73.5 - - - +
169D ASP* 1.3 56.6 + - - +
171D GLY* 2.9 19.6 + - - -
172D ILE 4.5 0.2 - - - -
174D PHE* 3.4 33.9 - + - -
195D ILE* 4.8 1.1 - - + -
198D ALA* 3.8 12.3 - - + -
199D VAL* 3.6 45.3 - - + -
205D ARG* 3.5 26.6 + - - +
206D ASN* 3.4 37.7 - - + +
209D LEU* 3.6 31.4 - - + +
210D LEU* 3.8 7.0 - - + -
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Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLU* 2.9 41.2 + - - +
166D THR* 3.3 8.5 + - - +
168D PHE* 1.3 76.2 - - - +
170D ASN* 1.3 61.9 + - - +
171D GLY 3.3 1.1 + - - -
205D ARG* 2.9 32.6 + - - +
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Residues in contact with ASN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D THR* 2.8 31.9 + - - +
167D LEU 3.1 5.7 + - - +
168D PHE 3.1 0.6 - - - -
169D ASP* 1.3 80.2 - - - +
171D GLY* 1.3 62.9 + - - +
172D ILE* 3.3 22.2 + - + +
336D ILE* 3.6 37.4 - - + +
339D SER* 5.3 2.3 + - - -
340D HIS* 5.1 3.6 + - - -
343D LYS* 6.1 0.5 - - - -
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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