Contacts of the helix formed by residues 184 - 194 (chain D) in PDB entry 2VD0
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 ILE 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.8 26.7 - - + -
140D TRP* 4.6 7.0 - - + -
146D VAL* 4.0 26.5 - - + -
151D PHE* 3.8 28.7 - - + -
180D LYS 3.5 8.4 + - - +
181D VAL* 3.2 20.6 + - - +
183D ALA* 1.3 74.3 - - - +
185D PRO* 1.4 65.1 - - + +
186D ALA* 4.2 7.6 - - + +
187D VAL* 2.9 11.2 + - + +
188D ALA 2.8 30.5 + - - -
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Residues in contact with PRO 185 (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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183D ALA 3.0 10.3 - - - +
184D ILE* 1.4 86.0 - - + -
186D ALA* 1.3 58.0 + - - +
187D VAL 3.2 0.2 + - - -
188D ALA* 3.2 6.8 + - + +
189D ASN* 2.9 44.0 + - - +
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Residues in contact with ALA 186 (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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23D ALA* 3.5 31.0 - - - +
24D TYR* 3.7 24.0 - - + +
184D ILE* 3.4 2.9 - - + +
185D PRO* 1.3 77.7 - - - +
187D VAL* 1.3 60.9 + - - +
189D ASN* 4.0 9.0 - - - +
190D TRP* 3.3 21.8 + - - +
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Residues in contact with VAL 187 (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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20D TYR* 3.9 33.4 - - + +
23D ALA* 5.4 0.7 - - - -
24D TYR* 4.9 3.4 - - + -
151D PHE* 3.9 34.3 - - + -
181D VAL* 3.6 23.1 - - + +
182D GLN* 4.3 2.7 - - + -
184D ILE* 2.9 17.9 + - + +
186D ALA* 1.3 77.4 - - - +
188D ALA* 1.3 65.7 + - - +
190D TRP* 3.1 6.7 + - + +
191D ILE* 2.9 41.1 + - + +
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Residues in contact with ALA 188 (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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182D GLN 3.4 21.3 + - - +
183D ALA* 4.5 4.9 - - - +
184D ILE 2.8 17.2 + - - +
185D PRO* 3.7 7.9 - - + +
187D VAL* 1.3 72.8 - - - +
189D ASN* 1.3 65.6 + - - +
191D ILE* 3.3 8.8 + - - +
192D LYS* 3.2 35.8 + - - +
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Residues in contact with ASN 189 (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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185D PRO* 2.9 30.7 + - - +
186D ALA* 4.0 8.5 - - - +
188D ALA* 1.3 79.4 - - - +
190D TRP* 1.3 58.1 + - - +
192D LYS* 3.0 18.7 + - - +
193D ARG* 2.9 28.1 + - - +
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Residues in contact with TRP 190 (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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16D GLU* 2.6 27.2 + - - -
19D ARG* 3.3 30.2 - - + +
20D TYR* 3.8 26.7 - + - -
23D ALA* 3.8 19.3 - - + -
29D TYR* 3.6 21.3 - + - -
31D ASP* 3.7 17.7 - - + -
33D ARG* 3.9 4.7 - - - -
186D ALA 3.3 15.6 + - - +
187D VAL* 3.1 7.0 + - - +
189D ASN* 1.3 79.1 - - - +
191D ILE* 1.3 56.7 + - + +
193D ARG* 4.3 18.8 - - + +
194D ARG* 2.8 65.6 + - + +
195D PRO* 4.7 1.8 - - + -
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Residues in contact with ILE 191 (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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20D TYR* 4.0 12.3 - - + +
154D GLU* 4.5 2.7 - - - +
182D GLN* 4.0 31.6 - - + +
187D VAL* 2.9 41.0 + - + +
188D ALA* 3.6 6.7 - - - +
189D ASN 3.3 0.2 - - - -
190D TRP* 1.3 74.2 - - + +
192D LYS* 1.3 60.7 + - + +
194D ARG* 3.8 47.1 + - - +
196D GLN* 5.1 6.1 - - - +
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Residues in contact with LYS 192 (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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188D ALA* 3.2 21.8 + - - +
189D ASN* 3.0 15.9 + - - +
191D ILE* 1.3 81.7 - - + +
193D ARG* 1.3 64.0 + - - +
194D ARG 3.5 5.1 + - - +
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Residues in contact with ARG 193 (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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189D ASN 2.9 15.7 + - - +
190D TRP* 4.0 21.7 - - + +
192D LYS* 1.3 78.9 - - - +
194D ARG* 1.3 64.4 + - - +
195D PRO* 3.7 3.1 - - - +
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Residues in contact with ARG 194 (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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12D ARG* 3.7 29.5 - - - +
16D GLU* 2.9 29.6 + - - +
20D TYR* 3.3 27.1 + - - -
33D ARG* 4.8 1.1 - - - +
154D GLU* 5.3 2.2 + - - -
158D THR* 5.1 9.5 - - - +
190D TRP* 2.8 50.6 + - + +
191D ILE* 3.8 40.0 + - - +
192D LYS 4.0 6.2 - - - +
193D ARG* 1.3 76.5 - - - +
195D PRO* 1.4 81.1 + - + +
196D GLN* 3.5 8.9 + - - +
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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