Contacts of the helix formed by residues 212 - 224 (chain B) in PDB entry 3H1J
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 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 5.2 11.2 - - - +
25B GLU* 3.0 37.3 + - - +
37B SER* 3.8 1.8 - - - -
39B GLU* 4.5 9.3 + - + +
211B VAL* 1.3 75.3 - - - +
213B HIS* 1.3 80.0 + - - +
214B SER* 2.9 35.9 - - - +
215B ASP* 2.9 35.2 + - - +
216B LEU* 3.2 10.9 + - - +
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Residues in contact with HIS 213 (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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25B GLU* 3.3 44.1 + - + +
26B ILE* 3.2 11.6 + - - -
27B THR* 2.8 41.5 + - - -
35B ILE* 2.8 39.0 - - + +
37B SER* 3.0 36.0 + - - +
212B LYS* 1.3 74.3 - - - +
214B SER* 1.3 57.1 + - - +
216B LEU* 4.6 0.9 - - - +
217B LYS* 2.8 39.7 + - + +
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Residues in contact with SER 214 (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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212B LYS* 2.9 36.1 - - - +
213B HIS* 1.3 75.8 - - - +
215B ASP* 1.3 62.8 + - - +
217B LYS* 3.9 7.3 - - - +
218B GLN* 3.1 25.8 + - - +
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B VAL* 5.5 3.3 - - + +
212B LYS* 2.9 32.0 + - - +
214B SER* 1.3 79.1 + - - +
216B LEU* 1.3 67.4 + - - +
217B LYS 3.1 1.3 - - - -
218B GLN* 3.1 24.7 + - - +
219B VAL* 3.2 18.8 + - + +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.8 13.5 - - + -
36B ALA 3.8 1.8 - - - +
37B SER* 3.7 21.5 - - - -
47B ILE* 4.6 14.8 - - + -
120B MET* 5.1 6.1 - - + -
206B LEU* 3.2 49.9 - - + +
208B GLY* 3.6 34.8 - - - +
211B VAL* 4.2 9.1 - - + +
212B LYS 3.2 9.8 + - - +
213B HIS 4.1 3.1 - - - +
215B ASP* 1.3 79.1 - - - +
217B LYS* 1.3 61.6 + - - +
219B VAL* 3.7 6.8 + - + +
220B ALA* 3.3 16.1 + - - +
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Residues in contact with LYS 217 (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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27B THR* 4.1 28.1 + - + +
29B LEU* 4.6 6.1 - - + -
35B ILE* 3.7 27.3 - - + +
213B HIS* 2.8 26.0 + - + +
214B SER* 3.9 6.1 - - - +
216B LEU* 1.3 75.1 - - - +
218B GLN* 1.3 69.6 + - - +
220B ALA* 2.9 13.9 + - - +
221B GLU* 3.0 35.5 + - - +
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Residues in contact with GLN 218 (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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214B SER 3.1 13.3 + - - +
215B ASP* 3.1 20.1 + - - +
217B LYS* 1.3 82.1 - - - +
219B VAL* 1.3 64.1 + - + +
221B GLU* 3.3 8.4 - - - +
222B GLN* 2.8 69.6 + - + +
223B PHE* 6.1 1.1 - - + -
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Residues in contact with VAL 219 (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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117B ASP* 6.0 2.5 - - - +
120B MET* 4.1 30.7 - - + -
124B LEU* 5.0 6.1 - - + -
206B LEU* 5.1 6.5 - - + -
215B ASP* 3.2 14.7 + - + +
216B LEU* 3.9 9.4 - - + +
217B LYS 3.2 0.8 - - - -
218B GLN* 1.3 82.6 - - + +
220B ALA* 1.3 67.0 + - - +
222B GLN 3.1 0.2 + - - -
223B PHE* 2.8 53.8 + - + +
224B LEU* 5.0 1.1 - - + +
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Residues in contact with ALA 220 (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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33B LEU* 3.5 20.0 - - + +
35B ILE* 3.4 26.9 - - + -
206B LEU* 3.7 13.2 - - + +
216B LEU 3.3 8.2 + - - +
217B LYS 2.9 9.9 + - - +
219B VAL* 1.3 77.9 - - - +
221B GLU* 1.3 57.4 + - - +
224B LEU* 3.0 44.0 + - - +
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Residues in contact with GLU 221 (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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29B LEU* 3.7 28.9 - - + +
217B LYS* 3.0 40.1 + - - +
218B GLN* 3.3 17.9 - - - +
220B ALA* 1.3 78.3 - - - +
222B GLN* 1.3 73.0 + - + +
223B PHE 3.3 1.2 + - - -
224B LEU 4.2 8.9 - - - +
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Residues in contact with GLN 222 (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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218B GLN* 2.8 63.5 + - - +
221B GLU* 1.3 87.1 + - + +
223B PHE* 1.3 81.8 + - + +
224B LEU 5.3 0.2 - - - -
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Residues in contact with PHE 223 (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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121B GLU* 6.3 2.5 - - + -
124B LEU* 3.1 41.2 - - + +
128B THR* 5.2 0.7 + - - -
218B GLN* 6.1 1.1 - - + -
219B VAL* 2.8 39.0 + - + +
222B GLN* 1.3 96.6 - - + +
224B LEU* 1.3 61.4 + - + +
225B ASN* 3.1 13.1 + - - +
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Residues in contact with LEU 224 (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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31B ASN* 6.2 0.2 - - - +
33B LEU* 3.2 42.0 - - + -
49B VAL* 6.2 3.6 - - + -
124B LEU* 3.7 13.7 - - + -
127B THR* 5.2 1.1 - - - +
128B THR* 3.4 33.4 - - + -
201B SER* 6.5 0.9 - - - -
204B MET* 4.7 11.9 - - + -
206B LEU* 5.0 8.5 - - + -
219B VAL* 5.0 0.9 - - + +
220B ALA* 3.0 24.8 + - + +
221B GLU 4.2 9.7 - - - +
222B GLN 5.3 0.2 - - - -
223B PHE* 1.3 74.3 - - + +
225B ASN* 1.3 70.8 + - - +
226B ILE* 5.3 5.2 - - + +
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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