Contacts of the strand formed by residues 253 - 257 (chain C) in PDB entry 1GG3
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 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C LEU* 6.2 0.2 - - - +
239C PHE* 4.8 8.5 - - + -
240C ILE 4.0 2.7 - - - +
241C LYS* 2.9 42.9 - - - +
251C GLU 4.5 1.0 + - - -
252C SER* 1.3 90.0 + - - +
254C ILE* 1.3 71.1 + - - +
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Residues in contact with ILE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ASP* 5.1 2.9 - - - +
197C LEU* 6.1 0.4 - - - -
223C PHE* 3.7 35.9 - - + -
239C PHE* 3.3 8.6 - - - +
240C ILE* 2.7 40.2 + - + +
241C LYS* 4.2 9.4 - - - -
242C ILE 5.1 3.8 - - - +
252C SER* 4.5 8.3 - - - +
253C THR* 1.3 91.2 - - - +
255C GLY* 1.3 71.3 + - - +
256C PHE* 3.3 32.1 - - + -
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Residues in contact with GLY 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ASP* 3.1 21.3 - - - +
197C LEU* 3.4 25.4 - - - +
238C PHE 3.1 12.1 - - - -
239C PHE* 3.6 11.4 - - - -
254C ILE* 1.3 82.1 - - - +
256C PHE* 1.3 67.5 + - - -
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA* 4.5 3.6 - - + -
195C LYS 3.2 17.0 - - - +
196C ASP* 4.1 20.4 - - + +
197C LEU* 4.9 4.4 - - - +
202C ILE* 4.3 7.9 - - + -
204C LEU* 3.8 46.7 - - + -
211C LEU* 5.1 0.7 - - + -
213C VAL* 4.2 26.2 - - + -
223C PHE* 4.4 7.4 - + - -
237C SER* 3.5 5.4 - - - -
238C PHE* 2.9 45.4 + + + +
239C PHE* 4.7 0.7 - - - -
240C ILE* 4.9 11.7 - - + -
254C ILE* 3.3 35.0 - - + -
255C GLY* 1.3 76.8 - - - -
257C LYS* 1.3 61.5 + - - +
258C LEU* 4.1 1.1 - - + -
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA 3.8 1.6 - - - -
195C LYS* 2.7 54.9 + - + +
196C ASP* 4.8 2.2 - - - +
197C LEU* 5.5 7.2 - - + -
199C GLY* 6.3 0.7 - - - -
236C SER* 3.0 27.8 + - - +
237C SER* 4.4 9.4 - - - +
256C PHE* 1.3 73.9 - - - +
258C LEU* 1.3 70.1 + - - +
259C PRO* 4.5 4.6 + - + +
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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