Contacts of the helix formed by residues 191 - 201 (chain I) in PDB entry 5GJQ
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 ASP 191 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I ILE 5.4 1.2 - - - +
190I LEU* 1.3 88.0 + - - +
192I ASN* 1.3 58.2 + - - +
193I GLN 2.8 1.3 - - - -
194I ILE* 2.1 48.5 + - - +
195I GLN* 3.0 5.2 + - - -
363I ARG* 3.7 32.9 + - - -
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Residues in contact with ASN 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398H ARG* 5.8 0.2 - - - -
190I LEU 3.3 3.2 + - - +
191I ASP* 1.3 78.7 - - + +
193I GLN* 1.3 62.1 + - - +
195I GLN* 3.7 19.4 + - - +
196I GLU* 3.0 52.1 + - - +
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Residues in contact with GLN 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I LEU* 3.7 33.8 + - + +
191I ASP 2.6 3.0 + - - +
192I ASN* 1.3 81.2 - - - +
194I ILE* 1.3 63.7 + - - +
196I GLU* 3.5 3.7 - - - +
197I ILE* 3.3 19.1 + - - +
235I LEU* 5.0 1.7 - - - +
351I ILE* 3.3 25.4 - - + +
352I GLU* 2.0 40.9 + - - +
353I PHE* 3.8 11.3 - - + -
354I PRO* 3.4 23.3 - - - +
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Residues in contact with ILE 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I TYR* 4.1 31.2 - - + +
187I ILE* 2.5 41.7 - - + -
190I LEU* 3.0 15.9 - - + -
191I ASP* 2.1 48.0 + - - +
193I GLN* 1.3 62.3 - - - +
195I GLN* 1.3 67.4 + - - +
196I GLU 3.0 0.9 - - - -
197I ILE* 2.8 25.0 - - + +
198I LYS* 2.9 10.9 + - + +
235I LEU* 3.3 16.6 - - + -
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Residues in contact with GLN 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H ARG* 3.2 42.6 + - - +
191I ASP 3.0 10.5 + - - +
192I ASN* 3.7 22.9 + - - +
194I ILE* 1.3 76.7 - - - +
196I GLU* 1.3 62.2 + - - +
198I LYS* 4.5 7.2 - - - -
199I GLU* 2.9 60.7 + - + +
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Residues in contact with GLU 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398H ARG* 3.2 23.1 + - - +
415H LYS* 3.0 28.9 + - - +
192I ASN* 3.0 42.3 + - - +
193I GLN* 3.5 2.0 - - - +
194I ILE 2.9 0.2 + - - -
195I GLN* 1.3 81.1 + - - +
197I ILE* 1.3 51.8 + - - +
199I GLU* 4.1 0.3 - - - +
200I SER* 2.7 36.6 + - - -
349I ARG* 3.0 24.5 + - - +
351I ILE* 3.4 27.1 - - + -
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Residues in contact with ILE 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I TYR* 4.8 2.7 - - - +
193I GLN 3.3 11.4 + - - +
194I ILE* 2.8 25.9 + - + +
196I GLU* 1.3 76.3 - - - +
198I LYS* 1.3 73.5 + - + +
200I SER* 2.5 24.0 + - - +
201I VAL* 2.8 29.7 + - + +
222I VAL* 4.1 19.7 - - + -
224I LEU* 5.1 4.0 - - + -
235I LEU* 3.1 46.9 - - + -
239I VAL* 4.8 6.1 - - + -
328I ILE* 4.8 13.0 - - + -
351I ILE* 3.6 10.9 - - + +
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Residues in contact with LYS 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I TYR* 3.6 23.3 - - + +
194I ILE* 2.9 18.3 + - + +
195I GLN* 4.2 5.4 - - - +
197I ILE* 1.3 78.1 - - - +
199I GLU* 1.3 59.9 + - + +
201I VAL 2.9 0.2 + - - -
202I GLU* 2.6 76.6 + - + +
203I LEU* 2.6 15.8 + - + +
242I GLN* 5.3 0.4 - - - +
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Residues in contact with GLU 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H MET* 3.3 14.1 - - - +
397H ILE* 5.7 2.6 - - + +
398H ARG* 2.6 61.8 + - - +
195I GLN* 2.9 42.2 + - + +
196I GLU 4.1 2.0 - - - +
198I LYS* 1.3 76.4 - - + +
200I SER* 1.3 54.1 + - - +
203I LEU* 3.1 23.3 - - + +
204I PRO* 2.7 27.2 - - - +
211I TYR* 3.0 12.8 + - - -
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Residues in contact with SER 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H MET* 3.7 5.2 - - - -
196I GLU 2.7 15.4 + - - -
197I ILE* 2.5 24.9 + - - -
199I GLU* 1.3 80.0 - - - +
201I VAL* 1.3 63.3 + - - +
204I PRO* 3.5 5.1 - - - +
218I PRO* 4.0 1.9 - - - +
219I PRO* 2.1 59.7 - - - +
222I VAL* 3.9 6.4 - - - +
326I LYS* 4.8 0.3 + - - -
349I ARG* 3.2 20.5 + - - +
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Residues in contact with VAL 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ILE* 2.8 21.3 + - + +
198I LYS 2.9 0.8 + - - -
200I SER* 1.3 90.4 - - - +
202I GLU* 1.3 68.7 + - + +
203I LEU 3.2 1.9 + - - -
204I PRO* 3.5 5.0 - - - +
205I LEU* 3.4 22.4 + - + +
219I PRO* 4.3 6.1 - - + +
220I LYS 5.0 1.1 - - - +
222I VAL* 4.0 19.1 - - + -
239I VAL* 5.1 6.5 - - + -
281I ILE* 5.0 15.0 - - + -
326I LYS* 4.5 35.9 + - + +
327I VAL 5.8 1.8 - - - +
328I ILE* 5.2 10.3 - - + -
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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