Contacts of the strand formed by residues 444 - 457 (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 PRO 444 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B PHE* 4.6 4.3 - - + -
398B TYR* 3.5 30.0 - - + -
401B ASN* 6.2 0.2 - - + -
402B LEU* 3.5 49.8 - - + +
437E TYR 3.5 8.3 - - - +
438E LEU* 3.7 11.6 - - + -
442E GLY 4.1 2.7 - - - +
443E ILE* 1.3 96.9 - - + +
445E ARG* 1.3 68.6 + - - +
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Residues in contact with ARG 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PHE* 5.0 0.5 - - - -
398B TYR* 4.9 3.4 + - - -
436E GLN* 3.5 4.3 - - - +
437E TYR* 2.9 62.9 + - + +
439E ASP* 4.1 24.3 + - + -
443E ILE* 3.1 43.0 + - - +
444E PRO* 1.3 77.7 + - - +
446E THR* 1.3 63.5 + - - +
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Residues in contact with THR 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO 4.9 0.2 - - - +
383B GLU* 3.1 36.5 + - + +
385B LEU* 3.7 28.6 - - + +
398B TYR* 4.1 10.1 - - - +
434E ILE* 3.6 21.0 - - - +
435E THR 3.3 7.8 + - - -
436E GLN* 4.6 5.1 - - - +
437E TYR* 4.1 4.8 + - - -
445E ARG* 1.3 78.1 - - - +
447E ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 3.8 4.9 - - - -
433E ARG 3.7 1.4 - - - +
434E ILE* 3.5 3.5 - - - -
435E THR* 2.9 38.6 + - - +
437E TYR* 3.9 20.2 - - + +
446E THR* 1.3 76.2 + - - +
448E GLN* 1.3 60.7 + - - +
449E SER* 5.1 1.3 + - - +
472E ALA* 4.3 17.7 - - + -
473E PRO 6.4 1.1 - - - -
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Residues in contact with GLN 448 (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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385B LEU* 3.4 31.3 - - + +
387B ASN* 3.0 29.9 + - - +
432E ILE* 3.5 31.4 - - + +
433E ARG 3.6 3.1 - - - +
434E ILE* 4.5 5.4 - - + +
447E ALA* 1.3 71.6 - - - +
449E SER* 1.3 71.0 + - - +
450E GLU* 3.0 23.0 + - - +
471E GLY 4.4 2.4 + - - -
472E ALA* 3.3 18.6 + - - +
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Residues in contact with SER 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E ILE* 3.5 8.3 - - - +
433E ARG* 2.9 53.1 + - - -
447E ALA* 5.1 1.4 + - - +
448E GLN* 1.3 76.9 + - - +
450E GLU* 1.3 65.3 + - - +
451E GLU* 4.1 2.7 - - - -
469E ARG* 4.0 21.5 - - - -
470E SER 3.3 9.4 - - - -
472E ALA* 3.3 21.4 + - - +
473E PRO 4.8 0.3 + - - -
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Residues in contact with GLU 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E TYR 3.8 4.7 - - - +
432E ILE* 4.4 15.0 - - + -
448E GLN* 3.0 38.2 + - - +
449E SER* 1.3 74.3 - - - +
451E GLU* 1.3 59.9 + - - +
452E THR* 5.4 0.6 + - - -
468E HIS 3.6 1.9 - - - +
469E ARG* 3.4 4.0 - - - -
470E SER* 2.5 61.7 + - - +
471E GLY 3.9 1.6 + - - -
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Residues in contact with GLU 451 (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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430E ALA* 3.3 4.2 - - - +
431E TYR* 2.8 76.3 + - + +
433E ARG* 2.8 45.7 + - + -
449E SER* 4.5 5.6 - - - -
450E GLU* 1.3 76.0 - - - +
452E THR* 1.3 62.9 + - - +
453E ARG* 3.7 12.9 + - - +
467E PHE* 4.3 11.9 - - + -
468E HIS 3.5 3.4 - - - +
469E ARG* 3.2 26.2 - - + -
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Residues in contact with THR 452 (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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428E CYS* 4.0 24.2 - - - -
429E ILE 3.5 4.9 - - - +
430E ALA* 3.8 13.0 - - + +
450E GLU 5.5 0.2 - - - -
451E GLU* 1.3 76.1 + - - +
453E ARG* 1.3 63.9 + - - +
454E VAL* 4.5 8.2 - - + +
466E HIS* 4.1 2.9 - - + +
467E PHE* 3.6 7.0 - - - -
468E HIS* 2.9 44.7 + - + -
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Residues in contact with ARG 453 (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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354E THR* 5.8 2.0 - - + -
357E LEU* 3.8 34.0 - - + +
361E ILE* 4.3 17.0 - - - +
369E TYR* 4.6 12.7 + - - -
377E MET* 6.0 0.2 - - - -
428E CYS* 3.3 5.4 - - - -
429E ILE* 2.8 43.6 + - + +
431E TYR* 3.9 24.6 + - + +
433E ARG* 5.3 2.8 - - - +
451E GLU* 3.7 15.3 + - - +
452E THR* 1.3 74.8 - - - +
454E VAL* 1.3 61.8 + - - +
455E TRP* 3.5 23.8 - - + +
464E ILE* 4.9 13.3 - - + +
466E HIS 3.9 2.2 - - - -
467E PHE* 3.3 53.1 - - - +
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Residues in contact with VAL 454 (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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422E MET* 5.2 7.0 - - + -
427E ALA 3.8 8.5 - - - +
428E CYS* 4.1 16.4 - - + +
452E THR* 4.5 7.0 - - + +
453E ARG* 1.3 76.3 - - - +
455E TRP* 1.3 64.7 + - - +
464E ILE* 3.5 4.1 - - - +
465E VAL* 2.9 48.1 + - + +
466E HIS* 3.1 36.0 + - + +
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Residues in contact with TRP 455 (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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350E ILE* 4.3 12.6 - - + -
353E VAL* 3.5 41.1 - - + -
354E THR* 4.0 22.6 + - + -
357E LEU* 4.0 16.8 - - + -
372E MET* 4.1 3.6 - - + -
422E MET* 5.2 0.2 - - - +
426E SER* 3.5 4.3 - - - -
427E ALA* 2.9 42.2 + - + +
429E ILE* 3.6 23.7 - - + +
453E ARG* 3.5 22.5 - - + +
454E VAL* 1.3 76.8 - - - +
456E HIS* 1.3 59.6 + - - +
462E TRP* 3.6 31.6 - - + -
463E GLN* 3.3 27.1 - - - -
464E ILE* 3.5 38.6 - - + -
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Residues in contact with HIS 456 (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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425E GLU* 2.8 41.2 + - + -
426E SER* 4.0 6.4 + - - +
455E TRP* 1.3 74.8 - - - +
457E ARG* 1.3 77.1 + - - +
458E ARG* 3.2 46.4 + - - +
461E LYS 3.4 2.8 - - - +
462E TRP* 3.5 4.0 - - - -
463E GLN* 2.9 37.2 + - + +
465E VAL* 4.6 21.3 - - + -
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Residues in contact with ARG 457 (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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346E ARG* 3.0 44.6 - - - +
349E GLU* 3.8 14.9 + - - -
424E ASP* 3.1 26.0 + - - +
425E GLU* 3.0 28.0 + - - +
456E HIS* 1.3 88.7 + - - +
458E ARG* 1.3 62.6 + - - +
459E ASP 5.1 0.2 - - - +
460E GLY* 4.3 13.5 - - - +
461E LYS 3.3 20.0 - - - +
462E TRP* 3.3 30.4 - - + +
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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