Contacts of the strand formed by residues 470 - 477 (chain B) in PDB entry 1IVV
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 PHE 470 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A PRO* 4.5 3.4 - - + -
284A TYR 4.9 0.2 - - - -
285A GLY* 3.6 24.2 + - - +
418A ASN* 2.9 12.8 + - - -
430A PHE* 3.8 15.7 - - + +
431A HIS* 3.5 40.8 - - - -
432A GLN* 3.8 23.6 - - + -
523A LEU* 3.6 42.8 - - + -
524A ALA 5.3 1.8 - - - -
591A THR* 3.9 4.9 - - + -
592A HIS 5.0 0.2 - - - -
593A PHE* 3.6 28.5 - + - -
456B VAL 3.5 11.0 - - - +
457B ARG* 4.7 2.5 - - - -
458B GLN* 3.2 6.7 - - - +
468B ASN 3.7 5.6 + - - +
469B ALA* 1.3 76.3 - - - +
471B SER* 1.3 63.1 + - - +
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ASP* 2.6 38.5 + - - +
430A PHE* 4.4 2.6 - - - -
593A PHE* 3.6 15.2 - - - -
455B VAL* 3.7 2.8 - - - +
456B VAL* 2.7 44.9 + - - +
458B GLN* 3.4 15.1 + - - -
470B PHE* 1.3 74.8 - - - +
472B ARG* 1.3 71.2 + - - +
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Residues in contact with ARG 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A SER* 4.7 7.5 - - - -
430A PHE* 3.9 22.2 - - + -
593A PHE* 3.3 57.4 + - + +
594A PRO 5.2 0.6 + - - -
453B GLU* 2.9 39.0 + - + +
454B ASP 3.2 13.2 - - - +
456B VAL* 3.7 5.7 - - - +
471B SER* 1.3 86.3 + - - +
473B LYS* 1.3 63.2 + - - +
474B ARG* 3.2 24.4 - - + +
513B LYS* 3.5 9.9 - - - +
614B GLU* 4.1 7.7 + - - -
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Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLU 3.6 1.1 - - - +
453B GLU* 3.3 4.5 - - - +
454B ASP* 2.9 61.4 + - + +
455B VAL 5.7 0.2 - - - -
456B VAL* 3.6 20.2 - - + +
472B ARG* 1.3 75.5 - - - +
474B ARG* 1.3 64.5 + - - +
475B THR* 4.3 12.6 - - - +
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Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B GLU* 3.4 40.0 + - + +
452B GLU 3.4 3.4 - - - -
453B GLU* 2.8 37.1 + - + +
472B ARG* 3.2 29.8 - - + +
473B LYS* 1.3 78.7 - - - +
475B THR* 1.3 62.5 + - - +
476B VAL* 4.1 2.6 + - - +
496B ILE* 3.4 21.6 - - + +
508B GLU* 5.6 4.0 + - - -
614B GLU* 3.4 20.4 + - - +
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B GLU* 3.0 4.6 - - - -
452B GLU* 2.8 45.6 + - - +
473B LYS* 5.0 13.9 - - - +
474B ARG* 1.3 74.1 + - - +
476B VAL* 1.3 73.4 - - - +
477B LEU* 3.5 11.5 + - + +
482B GLU* 5.3 2.7 - - - +
485B ARG* 5.4 7.6 - - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ARG* 3.6 31.2 - - + +
450B VAL 3.6 9.0 - - - +
451B GLU* 3.7 18.4 - - + +
474B ARG 4.2 1.8 + - - +
475B THR* 1.3 78.9 - - - +
477B LEU* 1.3 70.1 + - - +
478B THR* 3.4 11.1 + - + +
482B GLU* 3.2 12.5 - - - +
578B ASP* 3.8 33.4 - - + +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B VAL* 3.0 41.4 + - + +
452B GLU* 4.6 4.9 - - + +
475B THR* 3.9 17.0 - - + +
476B VAL* 1.3 76.9 - - - +
478B THR* 1.3 59.5 + - - +
479B ARG 3.8 1.3 - - - -
482B GLU* 3.4 27.1 - - + +
483B ALA* 4.2 3.4 - - + -
485B ARG* 3.5 46.2 - - + +
495B TRP* 4.7 6.3 - - + -
543B VAL* 4.2 13.7 - - + -
577B ILE* 3.4 33.3 - - + +
578B ASP* 4.4 0.3 + - - -
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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