Contacts of the strand formed by residues 461 - 471 (chain B) 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 LYS 461 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS* 3.2 41.4 - - - +
372B MET* 4.4 15.4 - - - +
456B HIS 3.6 0.2 - - - +
457B ARG* 3.9 3.0 - - - +
458B ARG* 2.9 32.4 + - - +
459B ASP* 4.1 5.2 - - + +
460B GLY* 1.3 79.1 - - - +
462B TRP* 1.3 71.6 + - - +
463B GLN* 3.6 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG* 6.0 5.6 - - + -
349B GLU* 3.1 40.1 + - + +
350B ILE* 3.8 21.1 - - + -
353B VAL* 4.2 20.8 - - + +
372B MET* 4.2 7.8 - - - +
421B LEU* 6.3 0.4 - - + -
423B GLY 5.5 1.3 - - - -
424B ASP 4.2 3.4 - - - -
425B GLU* 3.4 36.1 - - - -
426B SER* 3.6 10.1 - - - -
427B ALA* 3.8 17.3 - - + -
455B TRP* 3.7 36.1 - - + -
456B HIS 3.5 7.2 - - - -
457B ARG* 3.4 48.6 - - + +
460B GLY 5.5 1.6 - - - -
461B LYS* 1.3 82.3 + - - +
463B GLN* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B THR 4.7 0.8 + - - -
371B LYS* 2.9 28.7 + - - +
372B MET 3.3 6.3 - - - +
373B CYS 3.8 12.9 + - - -
374B ASP* 3.8 28.7 - - + +
375B PRO* 4.6 4.8 - - - +
455B TRP* 3.4 6.5 - - - -
456B HIS* 2.9 37.0 + - - +
458B ARG* 4.2 18.1 - - - +
461B LYS* 4.0 18.0 - - + +
462B TRP* 1.3 80.4 - - - +
464B ILE* 1.3 63.6 + - - +
465B VAL* 3.5 1.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 4.0 10.3 - - + -
372B MET 2.9 16.1 + - - +
373B CYS* 4.4 4.5 - - - -
374B ASP* 2.9 24.3 + - - +
377B MET* 3.6 30.2 - - - +
453B ARG* 3.6 26.5 - - + +
454B VAL 3.4 6.1 - - - +
455B TRP* 3.4 47.3 - - + +
463B GLN* 1.3 70.9 - - - +
465B VAL* 1.3 62.3 + - - +
466B HIS 3.6 21.3 - - - +
467B PHE* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASP* 4.2 9.6 - - + -
376B GLY 4.1 2.9 - - - +
377B MET* 3.1 8.3 - - - +
378B THR* 2.9 21.7 + - - +
454B VAL* 3.0 34.7 + - + +
456B HIS* 3.7 25.6 - - + +
458B ARG* 3.6 31.2 - - - +
463B GLN* 4.2 1.6 - - + +
464B ILE* 1.3 76.1 - - - +
466B HIS* 1.3 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MET* 4.1 0.7 - - - -
378B THR* 2.9 39.2 + - - +
380B PHE* 4.0 28.1 - + - -
388B LEU* 4.4 5.2 - - + -
452B THR* 5.9 1.8 - - + -
454B VAL* 3.0 45.0 + - + +
464B ILE* 3.5 5.8 - - - +
465B VAL* 1.3 88.0 - - + +
467B PHE* 1.3 82.4 + - - +
468B HIS* 4.3 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TYR* 3.7 14.1 - - - -
377B MET* 3.8 21.1 - - - -
378B THR 2.9 6.7 + - - -
379B ALA* 3.2 26.7 - - + -
380B PHE 2.9 23.4 + - - -
381B GLU* 4.2 14.6 - - + -
395B HIS* 3.4 32.5 - + - -
451B GLU* 6.4 0.4 - - + -
452B THR 3.2 14.4 - - - +
453B ARG* 3.2 36.1 - - - +
454B VAL* 5.3 0.2 - - - -
464B ILE* 4.2 2.2 - - + -
466B HIS* 1.3 82.9 - - - +
468B HIS* 1.3 68.7 + - - +
469B ARG* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B PHE* 3.2 41.5 + + + +
450B GLU 3.7 1.2 - - - +
451B GLU* 3.4 2.7 - - - -
452B THR* 2.8 50.0 + - + -
466B HIS* 4.3 10.3 - - - +
467B PHE* 1.3 77.7 - - - +
469B ARG* 1.3 72.6 + - - +
470B SER* 4.9 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ILE* 6.0 1.4 - - - +
380B PHE 2.9 11.9 + - - +
381B GLU* 2.5 31.7 + - + -
382B PRO* 3.3 23.2 - - + +
383B GLU* 2.6 30.6 + - - -
398B TYR* 6.1 0.8 - - - -
433B ARG* 4.8 8.9 - - - +
449B SER* 3.1 29.6 - - - +
450B GLU 3.2 3.8 - - - -
451B GLU* 3.3 23.6 + - + -
453B ARG* 4.6 7.3 - - - +
467B PHE* 3.7 20.4 - - + -
468B HIS* 1.3 85.4 + - - +
470B SER* 1.3 62.7 + - - +
472B ALA 5.3 0.7 - - - +
473B PRO 4.1 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 4.1 7.4 - - - -
449B SER* 3.2 12.0 + - - -
450B GLU* 2.8 51.0 + - - +
468B HIS* 4.9 9.9 - - - -
469B ARG* 1.3 76.9 - - - +
471B GLY* 1.3 65.0 + - - +
472B ALA 4.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 3.4 16.0 - - - +
448B GLN 4.3 4.5 - - - -
450B GLU* 3.4 12.4 + - - -
470B SER* 1.3 78.6 + - - +
472B ALA* 1.3 68.5 + - - -
473B PRO* 3.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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