Contacts of the helix formed by residues 197 - 206 (chain V) in PDB entry 5XS0
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 197 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42L ALA* 3.4 23.1 - - + +
45L GLN* 2.7 27.1 + - - +
77L GLU* 4.4 14.0 + - - +
78L MET* 4.1 18.8 - - + +
192V LYS* 2.8 25.8 + - - +
195V ASP 3.5 3.1 + - - +
196V LEU* 1.3 77.8 - - - +
198V PRO* 1.3 66.7 - - - +
199V SER* 3.4 4.7 + - - -
200V VAL* 3.2 19.2 + - + +
201V GLU* 2.8 27.9 + - - +
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Residues in contact with PRO 198 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196V LEU* 3.7 25.4 - - + +
197V GLU* 1.3 89.8 - - - +
199V SER* 1.3 58.0 + - - +
201V GLU* 3.3 6.7 + - + +
202V GLU* 2.9 30.5 + - - +
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Residues in contact with SER 199 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ALA* 4.0 13.9 - - - +
197V GLU* 3.4 2.8 + - - -
198V PRO* 1.3 80.0 - - - +
200V VAL* 1.3 59.0 + - - +
202V GLU* 3.3 10.6 + - - +
203V ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 200 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLU* 5.0 2.5 - - + +
38L ALA* 3.6 37.2 - - + +
39L ILE* 3.5 17.3 - - + +
42L ALA* 4.0 5.2 - - + -
77L GLU 4.4 1.3 - - - +
78L MET* 3.5 14.4 - - + +
197V GLU* 3.2 32.0 + - + +
198V PRO 3.2 0.2 - - - -
199V SER* 1.3 78.4 - - - +
201V GLU* 1.3 58.5 + - - +
203V ALA* 3.4 2.1 + - - +
204V ARG* 2.9 55.4 + - - +
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Residues in contact with GLU 201 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L GLU* 5.2 2.0 - - - +
36M TYR* 3.2 35.3 + - - -
37M GLN* 5.1 4.7 - - - +
40M GLN* 3.9 15.6 + - - +
41M LYS* 5.5 11.6 + - - +
44M ARG* 4.7 11.5 + - - +
196V LEU* 5.0 10.5 - - + -
197V GLU 2.8 17.2 + - - +
198V PRO* 3.6 8.1 - - + +
200V VAL* 1.3 75.5 - - - +
202V GLU* 1.3 57.2 + - - +
204V ARG* 3.3 13.3 + - - +
205V TYR* 2.9 36.2 + - + +
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Residues in contact with GLU 202 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198V PRO 2.9 17.2 + - - +
199V SER* 3.7 8.1 + - - +
200V VAL 3.2 0.2 - - - -
201V GLU* 1.3 75.0 - - - +
203V ALA* 1.3 67.0 + - - +
204V ARG 3.2 0.2 + - - -
205V TYR* 3.2 6.0 + - - +
206V ASN* 2.8 43.2 + - - +
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Residues in contact with ALA 203 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L THR* 4.3 0.5 + - - -
34L GLU* 3.5 47.9 - - + +
35L GLU* 3.5 8.7 - - - +
38L ALA* 4.4 2.9 - - + -
199V SER 3.0 17.4 + - - +
200V VAL 3.9 2.7 - - - +
202V GLU* 1.3 77.7 + - - +
204V ARG* 1.3 57.2 + - - +
206V ASN* 3.4 9.0 + - - +
207V SER* 3.0 26.0 + - - -
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Residues in contact with ARG 204 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L GLU* 3.2 29.2 + - - +
77L GLU 2.9 25.9 + - - -
78L MET 3.0 18.6 + - - -
79L PHE 3.7 11.2 + - - -
80L GLY* 3.5 8.7 - - - -
82L ASN* 5.6 1.1 - - - -
116L LYS* 4.0 11.0 - - - +
36M TYR* 2.3 49.4 + - + +
40M GLN* 3.2 19.8 - - - +
200V VAL* 2.9 31.0 + - - +
201V GLU* 3.3 13.9 + - - +
203V ALA* 1.3 75.4 - - - +
205V TYR* 1.3 61.7 + - - +
207V SER* 2.8 25.2 + - - -
208V CYS* 3.3 13.5 - - - -
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Residues in contact with TYR 205 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ALA* 3.4 43.1 - - + +
34M GLU* 4.5 9.0 + - - +
36M TYR* 4.7 8.8 - + - -
37M GLN* 3.0 42.5 + - + -
201V GLU* 2.9 24.9 + - + +
202V GLU* 3.7 6.3 - - - +
204V ARG* 1.3 76.7 - - - +
206V ASN* 1.3 72.7 + - - +
207V SER 3.3 0.7 + - - -
208V CYS* 3.4 19.3 + - - +
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Residues in contact with ASN 206 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L THR* 5.6 0.2 - - - +
34L GLU* 4.6 11.3 - - - +
202V GLU* 2.8 40.8 + - - +
203V ALA* 3.5 9.1 + - - +
205V TYR* 1.3 89.6 - - - +
207V SER* 1.3 58.5 + - - +
208V CYS 3.3 5.3 + - - +
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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