Contacts of the strand formed by residues 462 - 470 (chain E) in PDB entry 5IG3
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 TRP 462 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346E ARG* 4.4 11.0 - - + -
349E GLU* 3.6 34.4 + - + +
350E ILE* 3.6 22.8 - - + +
353E VAL* 3.9 30.3 - - + +
371E LYS 5.3 0.2 - - - +
372E MET* 4.1 6.4 - - - +
423E GLY 5.8 1.1 - - - -
424E ASP 5.0 0.7 - - - -
425E GLU* 4.0 2.9 - - - -
426E SER 3.9 21.3 - - - -
427E ALA* 4.1 15.5 - - + -
455E TRP* 3.6 36.3 - - + -
456E HIS 3.5 4.7 - - - -
457E ARG* 3.3 62.2 - - + +
461E LYS* 1.3 76.9 - - - +
463E GLN* 1.3 65.6 + - - +
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Residues in contact with GLN 463 (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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370E THR 5.1 0.2 + - - -
371E LYS 3.2 22.4 + - - +
372E MET 3.3 11.2 - - - +
373E CYS 4.0 13.3 + - - -
374E ASP* 3.9 26.5 - - + +
375E PRO* 4.9 3.9 - - - +
455E TRP* 3.3 8.6 - - - -
456E HIS* 2.9 37.2 + - + +
458E ARG* 4.4 17.6 + - + +
461E LYS* 4.0 26.1 - - + +
462E TRP* 1.3 80.4 - - - +
464E ILE* 1.3 62.8 + - - +
465E VAL* 3.4 1.3 + - - +
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Residues in contact with ILE 464 (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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357E LEU* 3.7 27.6 - - + -
372E MET* 3.0 24.4 + - + +
373E CYS* 3.6 16.2 - - - -
374E ASP* 3.1 24.1 + - - +
377E MET* 3.6 28.6 - - - +
453E ARG* 4.9 10.3 - - + +
454E VAL 3.5 7.2 - - - +
455E TRP* 3.5 35.7 - - + -
463E GLN* 1.3 70.9 - - - +
465E VAL* 1.3 58.0 + - - +
466E HIS 3.5 26.5 - - - +
467E PHE* 4.4 6.5 - - + -
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Residues in contact with VAL 465 (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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374E ASP* 4.5 20.4 - - + +
376E GLY 4.4 5.1 - - - +
377E MET* 3.8 7.6 - - - -
378E THR* 3.5 17.7 + - - -
454E VAL* 2.9 35.1 + - + +
456E HIS* 4.6 23.6 - - + -
458E ARG* 6.3 0.4 - - - +
463E GLN 3.4 1.4 + - - +
464E ILE* 1.3 74.7 - - - +
466E HIS* 1.3 65.3 + - + +
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Residues in contact with HIS 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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378E THR* 3.0 34.3 + - - +
379E ALA 4.6 0.4 - - - -
380E PHE* 4.3 20.6 - + - -
388E LEU* 4.7 4.7 - - + -
452E THR* 5.3 2.5 - - + -
453E ARG* 3.9 0.9 - - - -
454E VAL* 3.1 49.0 + - + +
464E ILE* 3.5 10.7 - - - +
465E VAL* 1.3 86.3 - - + +
467E PHE* 1.3 79.1 + - - +
468E HIS* 3.9 19.1 - - + +
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Residues in contact with PHE 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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369E TYR* 5.6 0.7 - - - +
377E MET* 4.8 5.6 - - - -
378E THR 2.9 9.8 + - - +
379E ALA* 3.1 19.1 - - + -
380E PHE 2.9 25.4 + - - -
381E GLU* 3.3 27.6 - - + -
395E HIS* 4.1 10.1 - + - -
451E GLU* 4.3 10.5 - - + -
452E THR 3.6 4.7 - - - -
453E ARG* 3.3 54.1 - - - +
464E ILE* 4.4 7.0 - - + -
466E HIS* 1.3 82.4 - - - +
468E HIS* 1.3 72.8 + - - +
469E ARG* 3.3 44.4 - - + -
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Residues in contact with HIS 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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380E PHE* 3.3 39.7 - + + +
450E GLU 3.6 1.6 - - - +
451E GLU* 3.5 3.1 - - - -
452E THR* 2.9 50.8 + - + +
466E HIS* 3.9 13.9 - - + +
467E PHE* 1.3 79.0 - - - +
469E ARG* 1.3 74.9 + - - +
470E SER* 5.0 7.6 + - - -
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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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380E PHE 2.9 8.7 + - - +
381E GLU* 3.3 31.5 + - - +
382E PRO* 3.5 19.7 - - + +
383E GLU* 2.4 42.8 + - - -
433E ARG* 3.5 15.8 - - - +
449E SER* 4.0 11.0 - - - -
450E GLU 3.4 3.4 - - - -
451E GLU* 3.2 35.4 + - + -
467E PHE* 3.3 31.5 - - + -
468E HIS* 1.3 83.4 + - - +
470E SER* 1.3 70.0 + - - +
472E ALA 3.5 12.9 + - - +
473E PRO* 3.7 8.1 + - - +
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Residues in contact with SER 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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382E PRO* 4.3 2.2 - - - -
449E SER* 3.3 4.6 - - - -
450E GLU* 2.5 63.3 + - - +
468E HIS* 5.0 9.3 + - - -
469E ARG* 1.3 78.9 - - - +
471E GLY* 1.3 59.6 + - - +
472E ALA 3.7 2.0 - - - -
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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