Contacts of the strand formed by residues 164 - 167 (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 ASN 164 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ALA* 3.7 34.4 - - + +
150A ILE* 5.7 0.6 - - - +
158H PHE* 3.9 7.0 - - - -
159H SER* 2.7 38.5 + - - -
162H GLU* 3.1 9.1 - - + +
163H LYS* 1.3 81.6 - - - +
165H TRP* 1.3 95.0 + - - +
172H PHE* 4.1 17.9 - - + +
173H LEU* 3.3 30.0 + - - +
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Residues in contact with TRP 165 (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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156H LEU* 3.9 11.0 - - + -
157H ASN* 3.3 23.6 - - - -
158H PHE* 3.6 13.2 - + + -
164H ASN* 1.3 92.3 + - - +
166H LYS* 1.3 58.1 + - - +
172H PHE* 3.6 5.0 - - - -
173H LEU* 2.9 43.6 + - + -
180H ILE* 3.7 26.3 - - + +
184H ALA* 3.6 32.3 - - + +
188H SER* 3.6 33.0 - - - -
189H CYS* 4.0 0.4 - - - -
190H ILE* 3.7 35.0 - - + -
199H SER* 3.3 28.5 - - - -
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Residues in contact with LYS 166 (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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200A GLU* 4.7 5.9 + - - -
201A TYR* 5.5 10.1 - - - -
204A THR* 5.8 0.9 + - - -
156H LEU* 3.4 5.7 - - - -
157H ASN* 2.8 41.9 + - - +
159H SER* 4.0 23.0 + - - +
162H GLU* 5.4 1.2 + - - -
164H ASN 3.8 0.2 + - - -
165H TRP* 1.3 74.9 - - - +
167H TRP* 1.3 70.6 + - - +
168H ILE* 3.9 0.5 + - - +
170H GLY* 3.4 27.7 - - - -
171H SER 3.5 11.0 - - - +
172H PHE* 3.8 31.7 - - + +
502H NAG 5.3 6.1 + - - +
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Residues in contact with TRP 167 (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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130H LEU 3.7 7.9 - - - -
131H LEU* 3.6 21.1 - - + -
132H ILE* 3.3 47.6 - - + -
154H ILE* 4.1 10.8 - - + -
155H GLY 3.3 22.2 - - - -
156H LEU* 3.6 39.8 - - + +
166H LYS* 1.3 80.4 - - - +
168H ILE* 1.3 59.6 + - - +
169H ASN* 3.3 19.7 - - - +
170H GLY* 3.0 21.0 + - - -
171H SER* 2.7 25.4 + - - +
172H PHE 4.1 9.4 + - - -
173H LEU* 4.0 17.3 - - + +
174H ASN 5.1 1.0 - - - +
178H LEU* 4.0 10.8 - - + -
501H NAG 3.8 26.4 + - - -
502H NAG 4.3 3.6 + - - -
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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