Contacts of the helix formed by residues 199 - 211 (chain B) in PDB entry 3RLQ
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 GLU 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LYS* 3.6 24.6 + - - +
195B THR 4.5 2.0 - - - +
196B GLU* 2.9 34.0 + - - +
198B LEU* 1.3 78.3 - - - +
200B GLU* 1.3 65.3 + - - +
201B ARG* 4.4 11.9 - - + +
202B ARG* 3.2 14.0 + - + +
203B ILE* 3.0 25.5 + - - +
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Residues in contact with GLU 200 (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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224A LYS* 4.1 11.1 + - - +
82B PRO* 5.8 0.2 - - - -
198B LEU 3.7 3.0 + - - -
199B GLU* 1.3 72.7 - - - +
201B ARG* 1.3 84.3 + - - +
203B ILE* 3.4 4.7 + - - +
204B LYS* 2.7 63.6 + - - +
220B LEU* 4.0 22.3 - - + +
222B VAL* 4.2 17.9 - - + +
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Residues in contact with ARG 201 (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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199B GLU* 3.2 12.5 + - + +
200B GLU* 1.3 96.3 - - + +
202B ARG* 1.3 65.2 + - - +
204B LYS* 3.5 6.3 + - - +
205B GLU* 3.0 56.6 + - - +
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Residues in contact with ARG 202 (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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42B GLU* 2.6 37.9 + - - +
196B GLU* 2.8 58.1 + - - +
197B TYR* 3.9 11.4 + - + -
199B GLU* 3.2 12.3 + - + +
201B ARG* 1.3 84.6 - - + +
203B ILE* 1.3 63.7 + - - +
205B GLU* 2.7 61.3 + - - +
206B ILE* 3.0 42.0 - - + +
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Residues in contact with ILE 203 (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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226A LEU* 4.5 4.0 - - + -
45B LEU* 4.4 7.9 - - + -
80B LEU* 3.8 29.6 - - + -
82B PRO* 3.8 29.6 - - + -
89B LEU* 4.2 13.9 - - + -
197B TYR* 3.4 28.9 - - + +
199B GLU 3.0 20.8 + - - +
200B GLU* 3.8 4.9 - - - +
202B ARG* 1.3 76.1 - - - +
204B LYS* 1.3 63.4 + - - +
206B ILE* 3.3 8.9 + - + +
207B VAL* 3.0 25.7 + - + +
220B LEU* 4.0 17.9 - - + -
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Residues in contact with LYS 204 (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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224A LYS* 3.7 35.2 - - - +
226A LEU* 3.7 24.7 - - + -
200B GLU* 2.7 43.4 + - - +
201B ARG* 3.8 6.1 - - - +
203B ILE* 1.3 78.6 - - - +
205B GLU* 1.3 57.4 + - - +
207B VAL* 3.3 6.2 + - - +
208B LYS* 2.9 34.6 + - - +
220B LEU* 4.4 4.3 - - + -
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Residues in contact with GLU 205 (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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201B ARG* 3.0 53.0 + - - +
202B ARG* 2.7 59.5 + - - +
204B LYS* 1.3 79.1 - - - +
206B ILE* 1.3 58.5 + - - +
208B LYS* 3.7 10.3 - - - +
209B LYS* 2.9 31.0 + - - +
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Residues in contact with ILE 206 (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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42B GLU* 3.8 28.5 - - + +
45B LEU* 4.0 23.1 - - + -
46B ARG* 5.0 2.9 - - - +
197B TYR* 3.5 39.7 - - + -
202B ARG* 3.0 41.6 + - + +
203B ILE* 3.8 7.4 - - + +
205B GLU* 1.3 75.6 - - - +
207B VAL* 1.3 59.5 + - - +
209B LYS* 4.3 5.4 - - - -
210B HIS* 3.0 42.2 + - + +
211B SER* 4.8 0.3 + - - -
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Residues in contact with VAL 207 (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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226A LEU* 3.7 31.0 - - + -
227A GLU 5.6 0.4 - - - +
229A HIS* 4.2 13.2 + - + -
45B LEU* 4.2 10.8 - - + -
49B ILE* 4.2 7.9 - - + -
80B LEU* 3.9 19.1 - - + -
203B ILE 3.0 17.4 + - - +
204B LYS 3.7 3.8 - - - +
206B ILE* 1.3 73.2 - - - +
208B LYS* 1.3 61.8 + - - +
211B SER* 2.9 39.3 + - - -
212B GLN* 3.5 0.5 + - - -
218B ILE* 4.1 23.8 - - + -
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Residues in contact with LYS 208 (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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227A GLU* 3.4 38.4 + - + +
228A HIS* 6.4 1.1 - - + -
229A HIS* 6.5 0.2 - - - -
204B LYS* 2.9 22.4 + - - +
205B GLU* 3.7 8.3 - - - +
207B VAL* 1.3 77.8 - - - +
209B LYS* 1.3 54.8 + - - +
212B GLN* 2.6 29.4 - - + +
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Residues in contact with LYS 209 (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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42B GLU* 3.0 23.9 + - - +
205B GLU 2.9 18.5 + - - +
206B ILE* 3.8 4.7 - - - +
207B VAL 3.2 0.2 - - - -
208B LYS* 1.3 75.3 - - - +
210B HIS* 1.3 84.8 + - + +
212B GLN* 2.8 19.2 + - - +
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Residues in contact with HIS 210 (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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42B GLU* 2.8 33.5 + - + +
43B ILE* 4.6 8.7 - - + +
46B ARG* 3.7 59.2 + - + +
206B ILE* 3.0 30.0 + - + +
209B LYS* 1.3 102.7 + - + +
211B SER* 1.3 61.8 + - - +
212B GLN* 3.2 16.0 + - - +
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A HIS* 2.9 22.7 + - - -
45B LEU* 5.8 0.2 - - - +
46B ARG* 4.2 12.5 + - - +
49B ILE* 3.9 26.3 - - - +
206B ILE 4.8 0.2 + - - -
207B VAL* 2.9 30.7 + - - -
210B HIS* 1.3 81.8 + - - +
212B GLN* 1.3 61.0 + - - +
213B PHE 3.2 3.7 + - - +
214B ILE* 3.4 22.3 + - - +
218B ILE* 4.4 1.8 - - - -
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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