Contacts of the strand formed by residues 191 - 196 (chain H) in PDB entry 5FHX
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 LEU 191 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H LEU* 3.2 46.4 - - + +
183H TYR* 3.3 31.0 - - + -
184H ALA 5.0 0.4 - - - +
187H LEU* 3.1 40.6 + - + +
188H LYS 3.6 10.5 + - - +
189H SER 3.6 1.5 - - - +
190H ARG* 1.3 81.2 - - + +
192H SER* 1.3 61.7 + - - +
193H ILE* 5.0 4.9 - - + -
204H LEU* 5.4 7.2 - - + -
205H GLU 3.8 1.3 - - - +
206H MET* 3.7 38.8 - - + -
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Residues in contact with SER 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H TYR* 3.6 5.4 + - - -
190H ARG 5.4 0.2 - - - -
191H LEU* 1.3 74.4 - - - +
193H ILE* 1.3 64.7 + - - +
194H SER* 4.4 4.1 + - - -
203H PHE 4.3 0.3 - - - +
204H LEU* 3.6 4.3 - - - +
205H GLU* 2.8 53.1 + - - +
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Residues in contact with ILE 193 (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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160H TRP* 3.8 25.1 - - + +
172H LEU 4.7 1.1 - - - +
173H GLY* 3.7 39.3 - - - +
174H MET* 3.8 3.4 - - - +
175H ILE* 3.8 35.2 - - + +
181H ILE* 3.5 26.5 - - + +
182H ASP 4.2 1.3 - - - +
183H TYR* 3.1 30.7 + - + -
191H LEU* 5.0 4.7 - - + -
192H SER* 1.3 79.4 + - - +
194H SER* 1.3 64.8 + - - +
203H PHE 3.6 11.7 - - - +
204H LEU* 5.1 5.8 - - + -
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Residues in contact with SER 194 (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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175H ILE* 3.9 9.2 - - - -
181H ILE* 5.3 0.4 - - - -
192H SER* 5.1 3.8 + - - -
193H ILE* 1.3 75.0 - - - +
195H LYS* 1.3 61.1 + - - +
202H VAL* 3.5 5.7 - - - +
203H PHE* 2.7 54.0 + - - +
205H GLU* 6.2 0.2 - - - +
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Residues in contact with LYS 195 (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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153H LEU* 3.4 23.2 + - + +
154H THR* 4.1 3.6 - - - +
156H SER 5.5 0.9 - - - +
175H ILE* 3.8 26.6 - - + +
176H TRP 3.7 13.0 - - - -
177H GLY 3.1 29.6 + - - -
178H ASP 4.2 2.7 - - - +
179H GLY* 4.7 6.5 - - - +
194H SER* 1.3 77.9 - - - +
196H ASP* 1.3 60.5 + - - +
197H SER* 2.8 25.4 + - - +
201H GLN 3.3 11.9 - - - +
202H VAL* 3.9 11.9 - - + +
203H PHE* 4.2 4.3 - - - -
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Residues in contact with ASP 196 (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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153H LEU* 4.2 0.7 - - - -
195H LYS* 1.3 72.2 - - - +
197H SER* 1.4 57.0 + - - +
198H SER* 2.7 28.9 + - - -
199H LYS* 3.0 52.1 + - - +
200H SER 3.2 7.4 + - - -
201H GLN* 2.7 18.1 + - + +
203H PHE* 3.8 21.9 - - + -
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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