Contacts of the strand formed by residues 256 - 260 (chain G) in PDB entry 4IG9
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 ILE 256 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G LEU* 4.3 20.4 - - + +
253G CYS* 4.1 28.9 - - + +
255G LYS* 1.3 75.8 - - - +
257G ILE* 1.3 69.2 + - - +
258G VAL* 4.1 10.1 - - + -
338G LYS* 3.0 28.1 + - + +
339G LEU* 3.4 9.1 - - + +
340G LEU 2.8 25.2 + - - +
341G ARG 3.3 4.7 + - - -
434G ASP* 4.0 0.7 - - - +
435G LEU* 3.4 28.3 - - + +
437G ILE* 3.9 24.2 - - + -
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Residues in contact with ILE 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G LYS 3.8 0.2 + - - -
256G ILE* 1.3 77.6 - - - +
258G VAL* 1.3 63.9 + - - +
259G LEU* 3.5 26.5 - - + -
340G LEU* 3.9 13.0 - - + -
341G ARG* 3.3 7.6 - - + +
343G TYR* 3.7 21.3 - - + -
426G MET* 5.1 5.8 - - - -
429G ASP* 3.7 25.8 - - + +
433G VAL* 3.6 31.4 - - + -
435G LEU 2.9 6.9 + - - +
436G LEU* 3.5 14.3 - - + +
437G ILE 2.9 26.0 + - - -
451G ILE* 5.0 2.9 - - + -
455G ILE* 5.2 7.0 - - + -
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Residues in contact with VAL 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G ILE* 4.1 12.8 - - + -
257G ILE* 1.3 76.7 - - - +
259G LEU* 1.3 61.7 + - - +
260G THR* 3.7 24.0 - - + -
329G PHE* 5.7 4.7 - - + -
330G ILE* 3.7 16.2 - - + -
339G LEU* 3.7 23.1 - - + -
341G ARG 3.0 7.3 + - - -
342G ASN* 2.5 30.4 + - - +
343G TYR 3.0 11.4 + - - -
437G ILE* 3.3 15.7 - - + +
439G ILE* 3.7 22.7 - - + -
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Residues in contact with LEU 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G ILE* 3.5 27.1 - - + -
258G VAL* 1.3 69.6 - - - +
260G THR* 1.3 62.6 + - - +
261G GLY 4.2 0.2 + - - -
343G TYR* 3.3 10.5 - - + +
436G LEU* 4.0 7.2 - - + -
437G ILE 2.7 13.2 + - - +
438G VAL* 3.4 23.5 - - + +
439G ILE 2.8 24.9 + - - +
441G SER* 4.7 1.3 - - - -
443G LEU* 4.6 2.7 - - + -
448G VAL* 3.9 29.6 - - + +
451G ILE* 3.8 40.6 - - + -
452G PRO* 4.0 17.5 - - + -
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Residues in contact with THR 260 (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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258G VAL* 3.7 13.0 + - + -
259G LEU* 1.3 73.6 - - - +
261G GLY* 1.3 59.2 + - - +
264G VAL* 3.8 30.1 - - + -
327G HIS* 6.2 0.2 - - + -
330G ILE* 3.5 31.4 - - + -
342G ASN* 3.4 9.9 + - - +
343G TYR 3.0 5.1 + - - +
344G THR* 3.2 24.5 + - - -
345G GLN* 3.3 26.2 + - - +
351G GLU* 4.2 3.5 + - - -
439G ILE* 3.2 9.4 - - + +
441G SER* 4.3 2.9 - - - -
448G VAL* 5.5 1.3 - - - +
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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