Contacts of the helix formed by residues 179 - 189 (chain D) in PDB entry 2R2N
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS* 5.2 0.2 - - - +
176D SER 6.1 0.2 - - - -
178D TRP* 1.3 79.6 - - - +
180D PRO* 1.3 80.3 - - - +
181D GLU* 3.0 30.0 + - - +
182D ASP* 2.9 33.3 + - - +
183D ALA 4.3 0.9 + - - -
190D THR* 4.9 0.5 - - - +
222D LYS* 6.1 1.6 - - - +
223D TYR* 4.0 5.4 - - - -
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Residues in contact with PRO 180 (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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179D LYS* 1.3 97.3 - - + +
181D GLU* 1.3 74.4 + - + +
183D ALA* 3.3 22.0 + - - +
184D LYS* 4.7 2.8 + - - +
222D LYS* 3.4 55.2 - - + +
223D TYR* 3.8 20.1 - - + +
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Residues in contact with GLU 181 (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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179D LYS* 3.0 32.1 + - - +
180D PRO* 1.3 92.9 - - + +
182D ASP* 1.3 65.6 + - - +
183D ALA 3.1 2.1 + - - -
184D LYS* 3.2 36.3 + - - +
185D ASN* 4.1 3.1 + - - +
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Residues in contact with ASP 182 (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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59A LYS* 3.6 12.8 + - - -
178D TRP* 3.4 10.4 - - - +
179D LYS* 2.9 40.9 + - - +
181D GLU* 1.3 79.4 - - - +
183D ALA* 1.3 56.2 + - - +
184D LYS 3.2 0.2 - - - -
185D ASN* 2.9 31.2 + - - +
188D LYS* 3.6 33.7 + - + +
190D THR* 3.4 22.1 + - + +
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Residues in contact with ALA 183 (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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5D ARG* 3.4 29.8 + - - +
180D PRO 3.3 16.2 + - - +
181D GLU 3.1 0.4 - - - -
182D ASP* 1.3 78.4 - - - +
184D LYS* 1.3 61.6 + - + +
185D ASN 3.2 3.5 + - - +
186D PRO* 5.6 0.5 - - - +
190D THR* 3.3 19.0 + - + +
223D TYR* 3.6 24.0 - - + +
224D ASP* 4.0 16.6 - - + +
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 5.8 1.3 - - - +
180D PRO 4.8 2.9 - - - +
181D GLU* 3.2 32.7 + - - +
182D ASP 3.2 1.2 - - - -
183D ALA* 1.3 78.0 - - + +
185D ASN* 1.3 58.5 + - - +
186D PRO* 3.6 9.3 - - - +
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Residues in contact with ASN 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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181D GLU 4.8 1.8 - - - +
182D ASP* 2.9 16.8 + - - +
183D ALA 3.2 2.1 - - - +
184D LYS* 1.3 78.8 - - - +
186D PRO* 1.3 73.2 - - - +
187D GLN* 2.8 30.5 + - - +
188D LYS* 3.2 39.0 + - + +
189D ASN 4.4 1.2 + - - -
190D THR* 5.5 0.9 + - - -
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Residues in contact with PRO 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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5D ARG* 6.5 1.1 - - + -
183D ALA 5.1 1.1 - - - +
184D LYS 3.6 9.8 - - - +
185D ASN* 1.3 88.8 - - - +
187D GLN* 1.3 74.2 + - - +
188D LYS 3.4 0.5 + - - -
189D ASN* 3.5 12.8 + - - +
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Residues in contact with GLN 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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62A GLN* 5.4 5.5 - - - +
185D ASN* 2.8 26.2 + - - +
186D PRO* 1.3 90.4 - - - +
188D LYS* 1.3 58.7 + - + -
189D ASN* 3.1 6.3 + - - +
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Residues in contact with LYS 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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59A LYS* 4.6 9.6 - - - +
309A GLU* 2.4 37.4 + - - -
178D TRP* 2.8 26.5 + - + -
182D ASP* 3.6 49.7 + - + +
185D ASN* 3.2 41.1 + - + +
187D GLN* 1.3 74.6 - - + +
189D ASN* 1.3 63.3 + - - +
190D THR* 3.3 1.1 - - + -
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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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62A GLN* 4.3 23.7 + - - +
132D GLY 2.8 25.1 + - - -
133D ASP* 3.6 13.3 - - - +
134D ASN* 2.9 46.9 + - - +
155D ASN* 4.6 0.8 + - - -
178D TRP* 3.3 7.3 - - - -
185D ASN 4.4 0.4 + - - -
186D PRO 3.5 11.5 + - - +
187D GLN 3.1 8.1 - - - +
188D LYS* 1.3 81.3 - - - +
190D THR* 1.3 69.2 + - - +
192D LYS* 5.6 1.0 - - - +
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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