Contacts of the strand formed by residues 464 - 473 (chain A) in PDB entry 5IG0
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 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A PRO* 4.1 9.4 - - + -
351A ALA* 4.2 6.7 - - + +
352A VAL* 3.1 36.8 - - + +
355A VAL* 4.6 18.2 - - + +
373A THR 4.6 0.5 - - - +
374A MET* 3.9 9.4 - - - +
422A MET* 3.6 22.4 - - + -
425A ASP 3.7 8.3 - - - -
427A ALA* 3.8 11.9 - - + -
454A TRP* 4.0 24.1 - - + -
455A VAL 3.4 28.3 - - - -
456A LYS* 3.3 42.8 - - + -
457A ASP 3.8 1.9 + - - +
460A PHE* 3.5 16.8 - - - +
462A PHE* 3.2 26.3 + - - +
463A GLY* 1.3 81.2 + - - +
465A LYS* 1.3 60.3 + - - +
504A GOL 3.1 24.7 + - - -
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A MET 3.3 4.7 - - - +
376A ASP* 3.4 28.1 + - + +
454A TRP* 3.3 6.6 - - - -
455A VAL* 2.9 53.0 + - - +
456A LYS 4.7 0.4 - - - -
457A ASP* 3.1 26.5 + - + +
460A PHE* 3.6 38.2 - - + -
464A TRP* 1.3 76.5 - - - +
466A LEU* 1.3 61.9 + - - +
467A VAL* 3.6 18.6 + - + +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A LEU* 3.6 15.7 - - + -
371A TYR* 5.2 0.2 - - - +
374A MET 2.9 13.2 + - - +
375A VAL* 4.2 12.1 - - + -
376A ASP* 2.9 24.8 + - - +
379A VAL* 3.9 9.9 - - + +
452A ARG* 3.4 37.7 - - - +
453A VAL 3.5 20.4 - - - +
454A TRP* 3.3 32.0 - - + -
465A LYS* 1.3 71.4 - - - +
467A VAL* 1.3 59.1 + - - +
468A HIS 3.6 19.1 - - - +
469A PHE* 3.7 15.7 - - + -
501A SO4 4.9 0.7 - - - +
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Residues in contact with VAL 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ASP* 4.2 12.6 - - + -
378A ASN 4.3 2.3 - - - +
379A VAL* 3.4 7.7 - - - +
380A THR* 3.1 21.7 + - - +
453A VAL* 3.0 26.5 + - + +
455A VAL* 3.8 31.0 - - + -
465A LYS* 4.0 25.6 - - + +
466A LEU* 1.3 77.9 - - - +
468A HIS* 1.3 65.4 + - + +
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Residues in contact with HIS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A VAL* 4.2 0.9 - - - +
380A THR* 2.8 32.3 + - - +
382A PHE* 4.4 11.3 - + - -
390A LEU* 3.8 23.3 - - + -
451A THR* 5.4 2.5 - - + -
453A VAL* 2.8 49.5 + - + +
466A LEU* 3.6 4.2 - - - +
467A VAL* 1.3 87.4 - - + +
469A PHE* 1.3 86.0 + - - +
470A HIS* 4.2 11.1 - - + +
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Residues in contact with PHE 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A TYR* 4.4 2.2 - - - -
379A VAL* 4.3 6.3 - - + -
380A THR 3.1 6.2 + - - -
381A CYS* 3.1 31.3 - - + +
382A PHE 3.0 25.3 + - - -
383A GLU* 3.4 20.2 - - + -
397A HIS* 3.6 20.0 - + - -
450A GLU* 4.8 1.3 - - - -
451A THR 3.1 14.6 - - - +
452A ARG* 3.5 32.3 - - - -
466A LEU* 3.7 13.9 - - + -
468A HIS* 1.3 86.4 - - - +
470A HIS* 1.3 64.4 + - - +
471A ARG* 3.9 14.1 - - + -
501A SO4 3.2 37.9 - - - -
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Residues in contact with HIS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE* 3.3 40.2 - + + +
449A GLU 3.6 1.4 - - - +
450A GLU* 3.4 3.7 - - - -
451A THR* 2.8 49.5 + - - +
468A HIS* 4.2 9.9 - - + +
469A PHE* 1.3 75.6 - - - +
471A ARG* 1.3 67.6 + - - +
472A SER* 4.3 19.6 + - - -
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Residues in contact with ARG 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE 2.8 11.6 + - - +
383A GLU* 2.7 37.3 + - + -
384A PRO* 3.5 17.4 - - + +
385A GLU* 3.6 4.6 + - - -
433A ARG* 3.8 22.5 - - - +
448A TYR* 3.8 24.9 - - + -
449A GLU 3.3 3.4 - - - -
450A GLU* 2.6 41.4 + - + +
452A ARG* 3.7 2.8 - - - +
469A PHE* 3.9 6.2 - - + -
470A HIS* 1.3 78.7 + - - +
472A SER* 1.3 64.6 + - - +
501A SO4 2.9 30.4 + - - -
502A GOL 2.6 37.4 + - - -
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Residues in contact with SER 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A PRO* 4.9 2.7 - - - -
448A TYR* 3.2 7.1 - - - -
449A GLU* 2.9 56.3 + - - +
470A HIS* 4.3 17.1 + - - -
471A ARG* 1.3 76.8 - - - +
473A GLY* 1.3 66.7 + - - +
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Residues in contact with GLY 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A PRO* 4.8 4.8 - - - +
446A THR* 5.2 1.6 - - - -
447A ARG 3.8 0.4 - - - -
448A TYR* 3.4 26.1 - - - -
449A GLU* 6.1 1.0 - - - -
472A SER* 1.3 79.6 + - - +
474A ALA* 1.3 68.1 + - - +
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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