Contacts of the helix formed by residues 194 - 207 (chain L) in PDB entry 3A68
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 GLY 194 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190E ARG* 3.2 34.9 - - - +
192L GLY 3.8 0.2 + - - -
193L LYS* 1.3 72.9 - - - +
195L HIS* 1.3 66.9 + - - -
196L GLY 3.2 1.5 + - - -
197L VAL* 3.3 6.2 + - - +
198L TRP* 3.0 22.7 + - - +
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Residues in contact with HIS 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ARG 3.7 3.8 + - - -
191E VAL* 3.7 24.3 + - + +
195E HIS* 3.6 43.7 + + - +
196E GLY* 3.7 22.2 + - - -
199E HIS* 2.9 30.2 + - + +
193L LYS 3.7 1.8 + - - -
194L GLY* 1.3 71.4 - - - -
196L GLY* 1.3 56.9 + - - +
198L TRP* 3.3 13.2 + + - +
199L HIS* 2.9 26.1 + - + +
195P HIS* 3.7 22.4 + + + +
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Residues in contact with GLY 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191L VAL* 3.4 32.6 + - - +
192L GLY 3.6 9.7 + - - -
193L LYS 4.3 2.0 + - - -
194L GLY 3.2 1.0 - - - -
195L HIS* 1.3 78.9 - - - +
197L VAL* 1.3 56.6 + - - +
199L HIS* 3.2 3.6 + - - +
200L PHE 2.9 24.8 + - - -
195P HIS* 3.8 17.7 + - - -
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Residues in contact with VAL 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ARG* 3.9 21.8 - - - +
77L LEU* 4.2 9.2 - - + -
80L LEU* 6.0 0.4 - - + -
126L LYS 6.0 0.7 - - - +
127L GLY* 6.6 0.2 - - - -
128L ASP* 5.9 0.2 - - - +
129L ALA* 3.7 27.4 - - + -
130L LEU* 5.7 2.5 - - + +
188L LEU* 4.0 18.6 - - + +
191L VAL* 4.3 5.2 - - + -
192L GLY 3.1 22.7 + - - +
193L LYS* 3.8 15.9 - - + -
194L GLY 3.3 9.7 + - - +
196L GLY* 1.3 74.8 - - - +
198L TRP* 1.3 59.0 + - - +
200L PHE* 3.3 6.2 + - - +
201L ASP* 2.9 27.5 + - + +
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Residues in contact with TRP 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLN* 2.8 45.3 + - + +
190E ARG* 4.1 13.7 - - - +
191E VAL* 3.5 27.6 - - + -
199E HIS* 3.6 38.1 - + + -
200E PHE* 3.8 26.0 - + - -
203E MET* 3.8 22.9 - - + -
76L ALA 5.1 0.9 - - - -
77L LEU* 4.5 7.2 - - + -
194L GLY 3.0 13.3 + - - +
195L HIS* 3.6 11.9 - + - +
197L VAL* 1.3 78.4 - - - +
199L HIS* 1.3 63.4 + - - +
201L ASP* 3.2 10.5 + - - +
202L GLN* 2.9 57.6 + - + +
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Residues in contact with HIS 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E HIS* 3.5 32.2 + + + -
195L HIS* 2.9 17.4 + - + +
196L GLY 3.5 4.0 - - - +
198L TRP* 1.3 80.6 - - + +
200L PHE* 1.3 65.0 + - - +
202L GLN* 3.1 9.5 + - + +
203L MET* 3.0 21.4 + - + +
195P HIS* 2.9 24.9 + - + +
198P TRP* 3.6 21.1 - + + -
199P HIS* 3.5 42.3 + + - -
202P GLN* 5.6 1.6 - - - +
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Residues in contact with PHE 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L LEU* 4.4 6.1 - - + -
133L MET* 4.3 3.8 - - + -
184L TYR* 3.6 38.4 - + + -
187L GLN* 3.7 34.5 - - + -
188L LEU* 3.6 35.7 - - + -
191L VAL* 4.4 6.1 - - + -
196L GLY 2.9 13.5 + - - +
197L VAL 3.6 6.3 - - - +
199L HIS* 1.3 76.0 - - - +
201L ASP* 1.3 62.7 + - - +
203L MET* 3.1 31.5 + - + +
204L LEU* 2.9 45.0 + - + +
198P TRP* 3.8 15.3 - + + -
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Residues in contact with ASP 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ALA 5.0 0.3 - - - +
77L LEU* 3.3 27.5 - - + +
78L ARG* 3.2 9.2 + - - +
79L GLY* 2.8 22.8 + - - -
80L LEU* 2.7 43.9 + - + +
197L VAL 2.9 14.7 + - - +
198L TRP* 3.4 10.7 - - - +
200L PHE* 1.3 83.0 - - - +
202L GLN* 1.3 63.5 + - - +
204L LEU* 3.2 2.2 + - - +
205L LEU* 2.8 27.9 + - - +
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Residues in contact with GLN 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E HIS* 5.7 1.1 - - - +
203E MET* 3.3 22.8 - - - +
78L ARG* 3.0 26.2 + - - +
198L TRP* 2.9 53.7 + - + +
199L HIS* 3.1 13.9 + - + +
201L ASP* 1.3 81.2 + - - +
203L MET* 1.3 62.7 + - - +
205L LEU* 3.3 12.9 + - - +
206L HIS* 3.2 50.9 + - + -
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Residues in contact with MET 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L TYR* 4.8 6.7 - - + -
187L GLN* 3.7 15.0 - - - +
199L HIS* 3.0 13.1 + - + +
200L PHE* 3.1 50.0 + - + +
202L GLN* 1.3 75.9 - - - +
204L LEU* 1.3 63.5 + - + +
206L HIS* 3.2 4.8 + - - +
207L GLU* 2.8 41.8 + - - +
78P ARG* 3.8 17.9 - - - +
198P TRP* 3.9 11.4 - - + -
202P GLN* 3.3 29.8 - - - +
206P HIS* 6.1 0.2 - - + -
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Residues in contact with LEU 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L GLY* 3.8 19.9 - - - +
80L LEU* 4.0 27.8 - - + -
82L LYS* 4.6 7.1 - - - -
83L PHE* 3.9 20.4 - - + -
133L MET* 4.2 7.0 - - + -
184L TYR* 3.4 38.4 - - + +
200L PHE* 2.9 24.0 + - + +
201L ASP* 3.6 8.7 - - - +
203L MET* 1.3 81.3 - - + +
205L LEU* 1.3 64.5 + - - +
207L GLU* 3.3 33.3 + - - +
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Residues in contact with LEU 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L ARG* 4.0 53.6 - - + +
79L GLY* 3.7 8.9 - - - +
82L LYS* 3.4 37.5 - - + +
201L ASP 2.8 16.8 + - - +
202L GLN* 3.4 21.8 - - - +
204L LEU* 1.3 76.3 - - - +
206L HIS* 1.3 80.5 + - + +
207L GLU 4.8 0.2 - - - +
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Residues in contact with HIS 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L GLN* 3.2 45.0 + - + +
203L MET* 3.5 3.6 - - - +
205L LEU* 1.3 91.6 + - + +
207L GLU* 1.3 67.4 + - - +
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Residues in contact with GLU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L LYS* 5.3 6.1 + - - -
180L ARG* 3.1 25.9 + - - -
184L TYR* 2.5 32.6 + - - -
203L MET* 2.8 22.7 + - - +
204L LEU* 3.3 28.5 + - - +
205L LEU 3.4 1.4 - - - +
206L HIS* 1.3 84.5 - - - +
78P ARG* 5.3 6.6 + - - +
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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