Contacts of the helix formed by residues 197 - 206 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192P LYS* 2.6 29.5 + - - +
194P GLN* 5.5 0.2 + - - -
195P ASP 3.4 3.7 + - - +
196P LEU* 1.3 77.3 - - - +
198P PRO* 1.3 71.4 - - - +
199P SER* 3.4 2.8 - - - -
200P VAL* 3.2 19.5 + - + +
201P GLU* 2.9 22.0 + - - +
42Q ALA* 3.4 17.5 - - + +
45Q GLN* 2.6 31.5 + - - +
77Q GLU* 4.5 13.8 + - - +
78Q MET* 4.2 19.4 - - + +
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Residues in contact with PRO 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P GLN* 4.7 6.5 - - - +
196P LEU* 3.7 28.3 - - + +
197P GLU* 1.3 87.7 - - - +
199P SER* 1.3 58.3 + - - +
201P GLU* 3.3 7.3 + - + +
202P GLU* 2.9 30.0 + - - +
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Residues in contact with SER 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P GLU* 3.4 0.6 - - - -
198P PRO* 1.3 80.4 - - - +
200P VAL* 1.3 58.7 + - - +
202P GLU* 3.3 12.9 + - - +
203P ALA* 2.9 31.0 + - - +
38Q ALA* 4.2 12.8 - - - +
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Residues in contact with VAL 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197P GLU* 3.2 32.4 + - + +
199P SER* 1.3 78.6 - - - +
201P GLU* 1.3 56.7 + - - +
203P ALA* 3.4 2.5 + - - +
204P ARG* 2.9 56.0 + - - +
35Q GLU* 4.7 2.3 - - + +
38Q ALA* 3.6 37.2 - - + +
39Q ILE* 3.5 24.2 - - + +
42Q ALA* 4.1 5.6 - - + -
77Q GLU 4.6 2.2 - - - +
78Q MET* 3.6 4.7 - - + +
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Residues in contact with GLU 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196P LEU* 4.9 9.2 - - + -
197P GLU 2.9 17.0 + - - +
198P PRO* 3.6 7.9 - - + +
200P VAL* 1.3 75.9 - - - +
202P GLU* 1.3 58.2 + - - +
204P ARG* 3.4 10.4 + - - +
205P TYR* 2.9 30.9 + - + +
77Q GLU* 5.2 2.6 + - - +
36R TYR* 3.1 35.5 + - - -
37R GLN* 4.8 11.1 - - - +
40R GLN* 3.6 20.1 + - - +
41R LYS* 5.8 7.6 + - - +
44R ARG* 4.8 12.4 + - - +
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Residues in contact with GLU 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198P PRO 2.9 17.2 + - - +
199P SER* 3.7 10.7 + - - +
201P GLU* 1.3 75.2 - - - +
203P ALA* 1.3 65.3 + - - +
205P TYR* 3.2 6.8 + - + +
206P ASN* 2.9 42.1 + - - +
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Residues in contact with ALA 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P SER* 2.9 17.2 + - - +
200P VAL 3.9 2.9 - - - +
202P GLU* 1.3 77.4 + - - +
204P ARG* 1.3 56.5 + - - +
206P ASN* 3.4 10.2 + - - +
207P SER* 2.9 25.8 + - - -
32Q THR* 4.2 4.0 + - - -
34Q GLU* 3.6 22.5 - - + +
35Q GLU* 3.5 31.6 - - - +
38Q ALA* 4.7 2.0 - - + -
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Residues in contact with ARG 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P VAL* 2.9 35.7 + - - +
201P GLU* 3.7 11.6 + - - +
203P ALA* 1.3 74.5 - - - +
205P TYR* 1.3 61.2 + - - +
207P SER* 2.8 26.4 + - - -
208P CYS* 3.3 13.3 - - - -
35Q GLU* 2.9 31.3 + - - +
77Q GLU 3.4 5.9 + - - -
78Q MET 2.6 35.2 + - - -
79Q PHE* 3.4 17.1 + - - +
80Q GLY* 3.3 16.6 - - - +
82Q ASN* 5.3 1.6 - - - -
116Q LYS* 4.2 10.3 - - - +
36R TYR* 2.6 47.5 + - + +
40R GLN* 3.5 8.1 - - - +
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Residues in contact with TYR 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201P GLU* 2.9 24.0 + - + +
202P GLU* 3.2 7.2 + - + +
204P ARG* 1.3 77.5 - - - +
206P ASN* 1.3 75.0 + - - +
207P SER 3.3 1.0 + - - -
208P CYS* 3.5 18.1 + - - +
33R ALA* 3.3 43.7 - - + +
34R GLU* 4.3 9.4 + - - +
36R TYR* 4.5 6.6 - + + -
37R GLN* 3.1 44.0 + - + -
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Residues in contact with ASN 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202P GLU* 2.9 38.2 + - - +
203P ALA* 3.4 8.9 + - - +
204P ARG 3.2 0.2 - - - -
205P TYR* 1.3 89.8 - - - +
207P SER* 1.3 59.2 + - - +
208P CYS 3.3 4.9 + - - +
32Q THR* 5.5 0.3 - - - +
34Q GLU* 4.8 10.5 - - - +
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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