Contacts of the strand formed by residues 291 - 295 (chain G) in PDB entry 1F9E
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 GLN 291 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322F PRO* 3.5 25.0 - - + +
323F ASP* 3.2 10.6 - - - +
324F GLU* 2.5 64.0 - - - +
289G ASN 3.9 3.0 + - - -
290G TYR* 1.3 69.8 - - - +
292G LYS* 1.3 60.5 + - - +
334H VAL* 4.0 2.8 - - + +
337H CYS* 3.7 24.8 - - + +
338H VAL* 5.4 0.6 - - - +
383H GLY* 3.6 3.6 - - - -
384H LYS* 2.8 51.0 + - - +
385H GLN* 4.4 2.5 - - - +
386H MET* 4.3 12.4 - - + +
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Residues in contact with LYS 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU* 4.1 27.3 - - + +
322F PRO* 3.6 2.4 - - - +
323F ASP* 2.7 47.2 + - + +
290G TYR* 3.1 13.8 + - + +
291G GLN* 1.3 77.9 - - - +
293G GLY* 1.3 57.9 - - - +
382H MET 4.6 7.0 - - - +
384H LYS* 4.5 0.9 - - - -
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Residues in contact with GLY 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU* 4.5 4.9 - - - +
320F TYR* 4.4 16.0 - - - -
321F ILE 3.5 1.1 - - - -
291G GLN 4.0 0.4 + - - -
292G LYS* 1.3 76.7 - - - +
294G ILE* 1.3 68.2 + - - +
295G PRO* 4.6 1.6 - - - +
382H MET 4.5 5.9 + - - -
384H LYS* 3.4 28.1 - - - +
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Residues in contact with ILE 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E GLY* 3.2 28.9 - - - +
268E LEU* 3.5 27.1 - - + -
274E ALA* 3.5 28.0 - - + -
275E GLY 4.8 0.2 - - - +
320F TYR* 3.3 4.6 - - - -
321F ILE* 2.9 52.8 + - + +
322F PRO 4.3 6.3 - - - +
323F ASP* 3.8 20.0 - - + +
293G GLY* 1.3 80.8 - - - +
295G PRO* 1.3 70.4 - - + +
296G VAL* 4.5 0.9 - - + -
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Residues in contact with PRO 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU* 6.2 0.7 - - + -
274E ALA* 4.3 6.6 - - - +
318F THR* 4.5 8.1 - - - +
319F ARG 4.4 0.4 - - - +
320F TYR* 3.4 35.8 - - + +
293G GLY 4.6 2.0 - - - +
294G ILE* 1.3 83.6 - - + +
296G VAL* 1.3 73.1 + - - +
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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