Contacts of the strand formed by residues 197 - 201 (chain H) in PDB entry 5MGS
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 VAL 197 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138H LEU* 3.8 25.1 - - + -
178H LEU* 3.3 35.0 - - + +
179H GLU 4.5 0.6 + - - +
180H ILE* 3.8 19.5 - - + -
181H ARG* 3.0 34.2 + - - +
190H ILE* 3.5 26.9 - - + -
191H SER 3.4 5.2 - - - +
192H ILE* 4.0 12.6 - - + -
196H SER* 1.3 81.8 - - - +
198H TYR* 1.3 62.9 + - - +
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Residues in contact with TYR 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H LEU* 3.9 31.4 - - + -
180H ILE* 4.4 0.9 - - - -
181H ARG* 3.4 32.9 + - + -
189H CYS 3.7 0.3 - - - +
190H ILE* 3.4 11.6 - - - +
191H SER* 2.9 38.3 + - - +
193H SER* 4.0 8.3 + - - -
195H THR* 4.9 0.5 + - - -
196H SER* 3.1 32.5 + - - -
197H VAL* 1.3 79.7 - - - +
199H SER* 1.3 63.8 + - - +
200H GLU* 3.5 20.4 - - - +
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Residues in contact with SER 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H TRP* 3.3 25.3 - - - -
180H ILE* 4.0 5.3 - - - +
181H ARG 2.9 17.7 + - - +
182H GLY* 4.1 12.1 - - - -
183H ASP 2.7 28.7 + - - -
188H SER* 3.5 6.9 + - - -
189H CYS 3.6 4.9 - - - -
190H ILE* 3.9 2.5 - - - -
198H TYR* 1.3 75.0 - - - +
200H GLU* 1.3 66.0 + - - +
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Residues in contact with GLU 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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151H LEU* 3.3 24.0 - - - +
153H TRP* 3.6 20.2 - - + -
188H SER* 3.3 6.1 - - - -
189H CYS* 2.8 28.6 + - - +
191H SER* 3.2 34.4 + - - +
198H TYR* 3.5 13.5 - - - +
199H SER* 1.3 79.9 + - - +
201H TYR* 1.3 63.2 + - - +
204H THR* 4.6 13.5 + - - +
206H ILE* 4.9 2.5 - - + -
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Residues in contact with TYR 201 (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 TRP* 3.4 4.5 - - - -
185H LYS* 3.4 38.8 + - - -
186H GLU 5.1 2.7 - - - -
187H ASN* 3.4 16.2 - - + +
188H SER* 4.5 2.5 - - - +
200H GLU* 1.3 73.6 + - - +
202H CYS* 1.3 59.1 + - - +
203H SER* 3.9 14.1 - - - +
204H THR* 3.0 38.9 + - - +
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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