Contacts of the strand formed by residues 199 - 203 (chain B) in PDB entry 5GPY
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 LYS 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B LEU* 3.5 6.3 - - - +
168B LEU* 2.8 60.1 + - + +
169B GLU 4.8 0.2 + - - -
191B PHE* 4.3 24.2 - - + -
192B VAL 3.4 4.9 - - - +
193B ASN* 3.4 26.9 + - - +
197B LYS 3.7 8.8 + - - +
198B LYS* 1.3 74.9 - - - +
200B ILE* 1.3 61.7 + - - +
201B LEU* 4.7 4.7 - - + -
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU 3.5 17.5 - - - +
53A LYS* 3.4 30.1 - - + +
54A PHE* 3.8 16.2 - - + -
165B GLY* 3.8 4.0 - - - -
166B ILE 3.6 23.1 - - - +
167B LEU* 4.0 12.3 - - + +
190B LEU 3.4 1.2 - - - +
191B PHE* 3.3 7.3 - - - -
192B VAL* 2.8 38.8 + - + +
194B ARG* 3.6 21.3 - - + -
199B LYS* 1.3 77.7 - - - +
201B LEU* 1.3 66.2 + - - +
202B PHE* 3.5 20.8 - - + -
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.9 3.6 - - + -
155B LEU* 3.9 21.2 - - + +
164B GLY 4.7 1.0 - - - +
165B GLY* 3.6 1.9 - - - -
166B ILE* 2.8 41.6 + - + +
167B LEU 4.9 0.2 - - - -
168B LEU* 4.1 36.3 - - + -
171B ILE* 4.5 15.7 - - + -
182B VAL* 4.7 12.6 - - + -
189B ILE* 4.0 20.2 - - + -
190B LEU 3.4 2.9 - - - -
191B PHE* 3.4 35.0 - - + -
199B LYS* 4.5 1.3 - - + +
200B ILE* 1.3 75.9 - - - +
202B PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.5 42.4 - - + -
52A LEU* 3.5 42.0 - - + -
54A PHE* 4.4 2.5 - + - -
155B LEU* 4.4 6.1 - - - -
164B GLY* 4.3 5.8 - - - -
165B GLY* 3.5 27.6 - - - -
189B ILE* 3.5 4.9 - - - +
190B LEU* 2.7 48.5 + - + +
192B VAL* 3.9 11.0 - - + -
200B ILE* 3.5 25.1 - - + -
201B LEU* 1.3 75.3 - - - +
203B PHE* 1.3 66.8 + - - +
204B ASN 3.4 0.2 + - - -
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 5.3 1.9 - - - +
152B LEU* 3.9 26.5 - - + -
155B LEU* 3.3 32.1 + - + +
156B ASP* 3.9 37.0 - - + -
159B ASP* 3.8 35.2 - - + +
188B GLN* 3.9 12.8 - - + -
190B LEU* 4.0 8.0 - - - +
202B PHE* 1.3 76.8 - - - +
204B ASN* 1.3 76.9 + - - +
205B ASP* 3.5 19.4 + - + -
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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