Contacts of the strand formed by residues 465 - 470 (chain E) in PDB entry 4R2G
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 465 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E LYS* 4.1 5.8 + - - +
358E THR* 3.4 30.5 - - + +
360E VAL* 4.3 18.8 - - + -
462E GLU 4.1 8.7 - - - +
463E SER* 3.1 29.3 - - - +
464E GLU* 1.3 81.9 - - - +
466E GLU* 1.3 84.2 + - - +
467E ILE* 4.3 8.4 + - + +
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Residues in contact with GLU 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E PHE* 4.4 21.2 - - + -
357E LYS* 3.9 28.6 + - + +
358E THR 3.0 6.7 + - - -
359E ILE* 3.4 9.7 - - + -
360E VAL* 2.9 27.4 + - - +
456E ARG* 3.1 40.6 + - - +
458E GLY* 3.8 14.7 + - - -
465E ILE* 1.3 83.3 - - - +
467E ILE* 1.3 67.1 + - - +
468E PHE* 3.5 21.7 - - + -
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Residues in contact with ILE 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E VAL* 3.5 21.8 - - + +
362E THR* 3.6 30.1 - - + -
456E ARG* 3.0 5.2 - - - -
457E ASP* 2.9 63.2 + - + +
458E GLY 5.4 0.2 - - - +
465E ILE* 4.8 9.0 - - + +
466E GLU* 1.3 82.0 + - - +
468E PHE* 1.3 63.5 + - - +
469E ARG* 4.6 3.1 - - - +
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Residues in contact with PHE 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E ILE* 3.8 18.2 - - + -
349E LEU* 3.5 39.0 - - + -
353E PHE* 3.5 26.2 - + - -
359E ILE* 3.6 15.5 - - + -
360E VAL 2.8 14.0 + - - +
361E PHE* 3.4 23.3 - + + -
362E THR 3.0 24.1 + - - +
391E PHE* 5.4 0.3 - - - +
454E LEU* 4.5 12.6 - - + -
455E THR 3.3 7.4 - - - +
456E ARG* 3.5 27.1 - - + -
466E GLU* 3.5 28.0 - - + -
467E ILE* 1.3 74.6 - - - +
469E ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E THR* 3.2 27.1 + - + +
363E HIS* 2.9 34.8 + - - +
364E SER* 4.2 1.3 - - - -
365E SER* 2.6 38.6 + - - +
391E PHE* 5.8 0.2 - - - -
454E LEU* 3.1 9.2 - - - -
455E THR* 2.9 39.6 + - - +
457E ASP* 2.8 40.3 + - - +
467E ILE* 4.6 4.0 - - - +
468E PHE* 1.3 77.7 - - - +
470E PRO* 1.3 76.3 - - + +
48F PRO* 3.3 14.1 - - - +
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Residues in contact with PRO 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E GLN* 3.5 37.2 - - + +
362E THR 3.3 14.6 - - - +
363E HIS* 4.1 1.1 - - - -
364E SER* 3.9 28.1 + - - +
371E ILE 4.5 1.4 - - - +
387E SER* 4.8 0.9 - - - +
391E PHE* 3.6 41.1 - - + -
453E LEU 3.3 8.3 - - - +
454E LEU* 4.2 3.6 - - + -
455E THR* 5.2 1.9 + - - +
469E ARG* 1.3 92.3 - - + +
471E GLY* 1.3 58.1 + - - +
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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