Contacts of the strand formed by residues 196 - 200 (chain H) in PDB entry 4XLR
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 THR 196 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22H GLU* 4.9 15.0 - - + +
23H PHE 3.6 4.7 - - - +
24H VAL* 3.3 23.0 - - + +
179H PHE* 3.5 7.8 - - - +
180H GLN* 2.9 44.8 + - + -
182H GLU* 4.9 6.0 - - - -
194H LYS* 3.2 22.2 + - - -
195H LEU* 1.3 75.2 - - - +
197H LEU* 1.3 71.7 + - - +
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Residues in contact with LEU 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLY 3.7 0.7 - - - +
22H GLU* 3.2 30.2 - - - +
23H PHE* 3.3 43.5 + - + +
40H LEU* 6.0 4.9 - - + -
44H LEU* 4.5 11.4 - - + -
177H VAL* 3.7 27.8 - - + -
179H PHE* 4.2 20.4 - - + +
195H LEU* 6.0 2.7 - - + -
196H THR* 1.3 82.2 - - - +
198H ARG* 1.3 73.3 + - - +
199H ILE* 4.1 14.8 - - + -
211H LEU* 4.7 7.2 - - + -
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Residues in contact with ARG 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.3 26.7 - - + +
22H GLU* 4.3 5.6 - - + -
176H ARG* 3.1 27.4 - - - +
177H VAL* 2.8 38.6 + - - +
178H ALA* 2.9 26.1 + - - +
179H PHE* 5.0 1.7 - - - -
180H GLN* 4.7 17.5 + - + +
197H LEU* 1.3 76.1 - - - +
199H ILE* 1.3 59.1 + - - +
200H TRP* 4.0 15.9 - - + -
888J GLU* 4.0 16.9 + - - -
936J TYR* 4.8 7.5 + - - -
937J TYR* 2.4 39.3 + - - -
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Residues in contact with ILE 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H HIS 4.0 0.2 - - - +
20H TYR* 3.1 23.3 - - - -
21H GLY 3.3 20.6 + - - +
23H PHE* 3.5 24.7 - - + -
44H LEU* 3.7 40.6 - - + -
174H VAL* 3.6 22.7 - - + -
176H ARG 3.9 1.8 - - - -
177H VAL* 3.6 7.9 - - + -
197H LEU* 3.9 9.4 - - + -
198H ARG* 1.3 75.0 - - - +
200H TRP* 1.3 69.5 + - - +
201H THR* 5.2 0.7 - - + -
207H PRO* 3.6 26.0 - - + +
210H ALA* 4.5 2.7 - - + -
211H LEU* 4.8 1.8 - - - +
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Residues in contact with TRP 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H HIS* 3.7 6.5 - - + -
20H TYR* 3.3 48.0 - + - -
174H VAL* 3.1 26.0 - - - +
175H ARG* 3.6 28.7 - - + +
176H ARG* 3.0 50.3 + - + -
177H VAL 4.4 2.2 - - - -
198H ARG* 4.0 22.9 - - - -
199H ILE* 1.3 76.3 - - - +
201H THR* 1.3 70.3 + - - +
847J ASP* 4.8 6.1 - - - -
884J ARG* 3.1 32.1 - - - -
888J GLU* 4.3 15.9 - - - -
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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