Contacts of the strand formed by residues 443 - 457 (chain F) 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 ILE 443 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 5.6 0.4 - - - -
440A ALA* 6.2 4.5 - - + -
438F LEU* 3.5 2.0 - - - -
439F ASP* 2.7 38.4 + - - +
441F GLY* 4.7 8.5 - - - +
442F GLY* 1.3 78.3 - - - +
444F PRO* 1.3 83.4 - - + +
445F ARG* 3.4 31.2 + - - +
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Residues in contact with PRO 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A PHE* 4.0 14.1 - - + -
398A TYR* 3.6 30.0 - - + -
401A ASN* 6.0 0.2 - - + -
402A LEU* 3.6 48.5 - - + -
437F TYR 3.4 8.1 - - - +
438F LEU* 3.8 7.2 - - + -
442F GLY 3.6 3.6 - - - +
443F ILE* 1.3 94.8 - - + +
445F ARG* 1.3 70.8 + - - +
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Residues in contact with ARG 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PHE* 5.0 0.5 - - - -
398A TYR* 4.8 2.7 + - - -
436F GLN* 3.1 8.0 - - - +
437F TYR* 2.9 64.2 + - + +
439F ASP* 3.6 28.0 + - + -
443F ILE* 3.7 40.6 - - - +
444F PRO* 1.3 81.2 + - - +
446F THR* 1.3 64.2 + - - +
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Residues in contact with THR 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PRO 4.6 0.4 - - - +
383A GLU* 3.2 38.8 + - + +
385A LEU* 3.6 25.8 - - + +
398A TYR* 4.2 9.9 - - - +
434F ILE* 3.5 19.8 - - - +
435F THR 3.2 6.7 - - - -
436F GLN* 4.4 5.4 - - - -
437F TYR* 4.4 3.9 + - - -
445F ARG* 1.3 78.9 - - - +
447F ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 3.7 5.6 - - - -
433F ARG 3.6 1.4 - - - +
434F ILE* 3.3 6.1 - - - +
435F THR* 2.9 39.7 + - - +
437F TYR* 4.2 15.5 - - + +
446F THR* 1.3 75.6 + - - +
448F GLN* 1.3 59.9 + - - +
472F ALA* 4.1 22.9 - - + -
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Residues in contact with GLN 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 3.2 38.0 - - + +
387A ASN* 3.3 18.3 + - - +
432F ILE* 3.7 21.8 - - + +
433F ARG 3.6 3.1 - - - -
434F ILE* 3.7 16.4 - - + -
447F ALA* 1.3 75.1 - - - +
449F SER* 1.3 63.8 + - - +
450F GLU* 2.9 24.6 + - - +
471F GLY* 3.9 4.9 - - - -
472F ALA* 3.5 21.1 + - - +
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Residues in contact with SER 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432F ILE* 3.4 8.8 - - - +
433F ARG* 2.9 51.9 + - - -
448F GLN* 1.3 76.8 - - - +
450F GLU* 1.3 67.1 + - - +
451F GLU* 3.5 9.5 + - - +
469F ARG* 3.1 31.6 - - - +
470F SER 3.2 7.0 + - - -
472F ALA* 4.8 7.9 - - - -
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Residues in contact with GLU 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431F TYR 3.8 5.2 - - - +
432F ILE* 4.6 12.8 - - + -
448F GLN* 2.9 35.9 + - - +
449F SER* 1.3 73.9 + - - +
451F GLU* 1.3 60.5 + - - +
468F HIS 3.6 2.1 - - - +
469F ARG* 3.3 4.2 - - - -
470F SER* 2.9 63.2 + - - +
471F GLY* 4.1 3.6 + - - -
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Residues in contact with GLU 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F ILE* 4.4 0.5 - - - +
430F ALA* 3.3 3.1 - - - +
431F TYR* 2.5 84.1 + - + +
433F ARG* 2.6 47.2 + - + +
449F SER* 3.5 18.2 + - - +
450F GLU* 1.3 73.2 - - - +
452F THR* 1.3 62.8 + - - +
453F ARG* 3.3 22.1 + - - +
467F PHE* 5.6 2.0 - - + -
468F HIS 3.4 3.4 - - - +
469F ARG* 3.8 17.7 + - + -
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Residues in contact with THR 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428F CYS* 3.8 25.1 - - - -
429F ILE 3.6 4.9 - - - +
430F ALA* 3.7 13.9 - - + +
451F GLU* 1.3 76.6 + - - +
453F ARG* 1.3 63.2 + - - +
454F VAL* 4.5 8.3 - - + -
466F HIS* 4.2 1.1 - - + +
467F PHE* 3.2 8.3 - - - +
468F HIS* 2.8 49.4 + - + -
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Residues in contact with ARG 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F THR* 5.0 2.9 - - + +
357F LEU* 3.9 22.2 - - + +
358F ILE* 4.3 5.1 - - - +
361F ILE* 4.1 21.0 - - - +
369F TYR* 4.5 8.9 + - - -
428F CYS* 3.3 7.3 - - - -
429F ILE* 2.9 38.1 + - + +
431F TYR* 3.5 30.6 + - + +
433F ARG* 5.3 1.0 - - - +
451F GLU* 3.3 24.4 + - - +
452F THR* 1.3 75.4 - - - +
454F VAL* 1.3 61.8 + - - +
455F TRP* 3.7 14.3 + - + +
464F ILE* 3.5 24.1 - - + +
466F HIS 4.2 1.3 - - - -
467F PHE* 3.3 50.5 - - - +
469F ARG* 5.3 4.0 - - - +
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Residues in contact with VAL 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F MET* 5.3 6.1 - - + -
426F SER* 5.3 2.2 - - - +
427F ALA 3.8 9.6 - - - +
428F CYS* 3.9 17.3 - - + -
452F THR* 4.5 8.5 - - + +
453F ARG* 1.3 76.5 - - - +
455F TRP* 1.3 64.0 + - - +
456F HIS* 6.1 0.2 - - + -
464F ILE* 3.4 5.0 - - - +
465F VAL* 2.9 46.8 + - + +
466F HIS* 3.2 34.0 + - + +
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Residues in contact with TRP 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F ILE* 3.5 23.8 - - + +
353F VAL* 3.5 47.8 - - + -
354F THR* 3.3 35.4 + - + -
357F LEU* 3.9 14.8 - - + -
372F MET* 4.1 8.1 - - + -
426F SER* 3.4 6.4 + - - -
427F ALA 2.9 37.3 + - - +
429F ILE* 3.4 19.1 - - + +
453F ARG* 3.7 7.3 - - + +
454F VAL* 1.3 77.0 - - - +
456F HIS* 1.3 60.8 + - - +
462F TRP* 3.8 19.1 - - + -
463F GLN* 3.3 32.3 - - - -
464F ILE* 3.3 35.4 - - + -
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Residues in contact with HIS 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F GLU* 2.6 48.0 + - + -
426F SER* 3.9 10.1 - - - +
454F VAL* 6.1 0.4 - - + -
455F TRP* 1.3 77.8 - - - +
457F ARG* 1.3 71.9 + - - +
458F ARG* 3.4 45.7 + - - +
461F LYS 3.3 3.1 - - - +
462F TRP* 3.7 4.9 - - - -
463F GLN* 2.9 34.1 + - + +
465F VAL* 5.0 16.8 - - + -
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Residues in contact with ARG 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F ARG* 4.2 21.2 - - - +
349F GLU* 5.0 4.6 - - - +
424F ASP* 3.9 17.0 + - - +
425F GLU* 2.8 35.0 + - + +
456F HIS* 1.3 82.4 + - - +
458F ARG* 1.3 60.2 + - - +
460F GLY* 4.1 12.7 - - - +
461F LYS 3.3 21.4 - - - +
462F TRP* 3.2 49.7 - - + +
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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