Contacts of the helix formed by residues 179 - 189 (chain B) in PDB entry 3DC1
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 LYS 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B TRP* 1.3 81.4 - - - +
180B PRO* 1.3 71.0 - - - +
181B GLU* 3.0 27.9 + - - +
182B ASP* 3.0 40.0 + - - +
183B ALA 4.4 0.7 + - - -
190B THR* 4.7 0.3 - - - +
223B TYR* 4.1 2.9 - - - -
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Residues in contact with PRO 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TRP 4.2 3.4 - - - +
179B LYS* 1.3 94.3 - - + +
181B GLU* 1.3 72.6 + - + +
182B ASP 3.2 1.6 - - - -
183B ALA* 3.4 21.6 - - - +
184B LYS* 5.1 2.4 - - - +
222B LYS* 3.7 56.0 - - + +
223B TYR* 4.0 14.3 - - + +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS* 3.0 37.1 + - - +
180B PRO* 1.3 90.1 - - + +
182B ASP* 1.3 60.4 + - - +
183B ALA 3.1 6.5 + - - -
184B LYS* 3.2 46.3 + - - +
185B ASN* 4.6 3.1 - - - +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ARG 4.8 0.7 - - - +
178B TRP* 3.6 12.5 - - - +
179B LYS* 3.0 39.9 + - - +
181B GLU* 1.3 78.0 + - - +
183B ALA* 1.3 56.1 + - - +
184B LYS 3.2 0.7 - - - -
185B ASN* 3.1 28.2 + - - +
188B LYS* 3.2 39.9 + - + +
190B THR* 3.3 25.8 + - + -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.5 31.8 + - - +
180B PRO 3.4 17.3 + - - +
181B GLU 3.1 0.4 - - - -
182B ASP* 1.3 76.7 - - - +
184B LYS* 1.3 60.7 + - + +
185B ASN 3.1 6.2 + - - -
186B PRO 5.3 0.2 - - - -
190B THR* 3.8 15.8 + - + +
223B TYR* 4.4 11.9 - - + +
224B ASP* 3.9 29.1 - - + +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 6.1 0.4 - - - +
180B PRO 5.1 2.2 - - - +
181B GLU* 3.2 39.3 + - - +
182B ASP 3.2 1.0 - - - -
183B ALA* 1.3 80.6 - - + +
185B ASN* 1.3 58.5 + - - +
186B PRO* 4.3 4.7 - - - +
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Residues in contact with ASN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLU 4.6 2.5 - - - +
182B ASP* 3.1 22.3 + - - +
183B ALA 3.1 7.4 + - - -
184B LYS* 1.3 80.0 - - - +
186B PRO* 1.4 72.0 - - - +
187B GLN* 2.6 53.9 + - - +
188B LYS* 2.8 33.0 + - + +
189B ASN 4.2 0.7 + - - -
190B THR* 4.6 1.4 + - - -
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Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 6.2 4.9 - - + -
184B LYS 4.3 3.6 - - - +
185B ASN* 1.4 90.9 - - - +
187B GLN* 1.3 55.3 + - + +
189B ASN* 3.0 31.7 + - - +
190B THR* 5.6 1.6 - - - +
192B LYS* 6.2 2.0 - - - +
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASN* 2.6 36.9 + - - +
186B PRO* 1.3 74.2 - - + +
188B LYS* 1.3 70.4 + - - +
189B ASN* 3.1 4.7 + - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TRP* 3.0 18.1 + - + -
182B ASP* 3.2 51.5 + - + +
185B ASN* 2.8 30.8 + - - +
187B GLN* 1.3 88.8 - - - +
189B ASN* 1.3 67.8 + - - +
190B THR 2.9 2.8 + - - +
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLY 2.7 34.4 + - - -
133B ASP* 3.6 19.1 + - - +
134B ASN* 3.0 33.8 + - - +
178B TRP* 3.7 5.6 - - - -
185B ASN 4.2 0.6 + - - -
186B PRO* 3.0 19.7 + - - +
187B GLN 3.1 4.0 - - - +
188B LYS* 1.3 77.7 - - - +
190B THR* 1.3 69.5 + - - +
192B LYS* 5.0 5.5 + - - +
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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