Contacts of the strand formed by residues 582 - 592 (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 ILE 582 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B ASP* 3.7 5.0 - - - +
441B MET* 3.3 31.5 + - + +
446B PHE 4.3 1.0 + - - -
448B ASN* 3.9 11.2 - - + -
449B ARG* 3.7 24.0 - - - +
450B VAL* 3.5 32.8 - - + +
497B ILE* 4.7 1.6 - - + -
543B VAL* 3.9 9.9 - - + -
544B THR 3.2 5.8 - - - +
545B ARG* 4.6 0.9 - - - -
577B ILE* 3.4 44.4 - - + +
580B GLN* 3.1 14.8 + - + +
581B ASP* 1.3 77.4 + - - +
583B VAL* 1.3 68.8 + - - +
584B VAL* 5.1 0.7 - - + -
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Residues in contact with VAL 583 (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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438B ARG* 3.6 50.5 - - + +
439B LEU 3.4 11.9 - - - +
440B ASP* 3.9 15.5 - - - +
441B MET 4.5 0.2 - - - +
543B VAL* 3.2 5.1 - - - +
544B THR* 2.7 44.6 + - - +
546B TYR* 4.0 23.6 - - + -
550B GLU 5.9 0.2 - - - +
582B ILE* 1.3 80.2 - - - +
584B VAL* 1.3 64.9 + - - +
585B TRP* 3.6 14.7 - - + +
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ALA 3.5 1.9 - - - +
438B ARG* 3.6 1.2 - - - -
439B LEU* 2.7 57.6 + - + +
441B MET* 3.8 21.3 - - + -
450B VAL* 4.0 26.9 - - + -
497B ILE* 4.2 10.5 - - + -
514B LEU* 4.6 9.2 - - + -
541B LEU* 3.6 31.0 - - + -
542B TRP 3.5 3.1 - - - +
543B VAL* 4.4 8.3 - - + -
582B ILE* 5.1 0.9 - - + -
583B VAL* 1.3 76.5 - - - +
585B TRP* 1.3 64.9 + - - +
586B HIS 4.6 0.7 - - - +
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Residues in contact with TRP 585 (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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436B SER* 4.3 8.7 - - - +
437B ALA 3.3 6.1 - - - +
438B ARG* 3.5 47.8 - - + -
541B LEU* 3.6 3.6 - - - -
542B TRP* 2.7 57.1 + - + +
544B THR* 2.8 31.2 + - + +
550B GLU* 3.9 12.3 - - + -
551B ARG 3.8 13.0 - - - -
552B TYR 3.7 7.2 - - - -
553B PRO* 3.4 41.3 - - + -
567B LEU* 3.7 28.0 - - + -
570B TYR* 4.4 10.1 - + - -
583B VAL* 3.6 16.7 + - + +
584B VAL* 1.3 75.6 - - - +
586B HIS* 1.3 58.5 + - - +
587B THR 4.0 0.2 - - - -
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Residues in contact with HIS 586 (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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436B SER* 3.4 2.2 - - - -
437B ALA* 2.9 41.1 + - + +
439B LEU* 5.3 4.0 - - + -
495B TRP* 5.1 1.6 - + - -
514B LEU* 4.1 17.7 - - + +
516B ALA* 3.4 32.4 - - + +
517B HIS 5.0 0.4 - - - -
540B ASP* 2.8 32.8 + - + +
541B LEU* 4.2 15.0 - - + -
584B VAL* 4.0 4.3 - - + -
585B TRP* 1.3 72.8 - - - +
587B THR* 1.3 69.7 + - - +
588B PHE* 3.4 37.5 - - + +
608B GLY 4.6 0.4 - - - -
609B PHE* 3.8 27.6 - - + +
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Residues in contact with THR 587 (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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434B ILE* 3.7 24.0 - - + -
435B PHE 3.3 5.8 - - - -
436B SER* 4.5 0.9 + - - +
521B THR* 4.0 12.1 - - + +
536B PHE* 2.8 32.9 + - - -
537B ALA* 3.7 17.0 - - - +
539B LYS 3.0 20.7 + - - +
540B ASP* 2.9 16.5 + - - +
542B TRP* 4.1 4.3 + - - -
585B TRP 3.9 1.4 + - - -
586B HIS* 1.3 88.7 + - - +
588B PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 588 (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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277B ILE* 4.2 1.8 - - + -
398B PHE* 3.5 35.0 - + - -
400B ALA* 4.6 0.2 - - + -
434B ILE* 4.3 3.6 - - - -
435B PHE* 2.8 55.1 + + + -
437B ALA* 4.0 8.1 - - + -
517B HIS* 5.8 2.7 - - + +
519B GLN* 5.8 2.5 - - + +
521B THR* 6.0 1.1 - - - -
586B HIS* 3.4 40.2 - - + -
587B THR* 1.3 75.8 - - - +
589B GLY* 1.3 58.3 + - - +
607B VAL* 3.9 11.2 - - + -
608B GLY* 3.7 40.2 - - - +
609B PHE* 3.6 17.7 - + - -
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Residues in contact with GLY 589 (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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433B HIS 3.1 12.8 - - - -
434B ILE* 4.0 10.8 - - - +
519B GLN* 3.0 36.1 - - - +
520B PRO* 4.4 9.7 + - - +
587B THR* 5.5 0.2 - - - +
588B PHE* 1.3 76.2 - - - +
590B LEU* 1.3 62.9 + - - -
591B THR 4.2 0.3 + - - -
607B VAL* 3.8 11.8 - - - +
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Residues in contact with LEU 590 (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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400B ALA 5.4 0.9 - - - +
402B ALA* 4.4 14.6 - - + -
432B GLN* 3.1 8.3 + - - +
433B HIS* 2.8 48.7 + - + +
435B PHE* 5.6 1.8 - - + -
519B GLN* 4.9 10.5 - - - +
589B GLY* 1.3 74.0 - - - +
591B THR* 1.3 62.7 + - - +
592B HIS* 3.9 2.6 + - + -
602B MET* 5.8 0.4 - - + -
605B ASP* 3.7 40.4 - - + +
606B THR 3.3 30.7 - - - +
607B VAL* 3.7 22.2 - - + -
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Residues in contact with THR 591 (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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455A VAL* 4.1 7.6 - - + -
470A PHE* 3.9 17.7 - - + -
431B HIS 3.9 2.9 - - - +
432B GLN* 3.5 17.7 + - + -
519B GLN* 5.5 3.2 - - - +
520B PRO* 3.9 24.8 + - - +
523B LEU* 4.0 10.5 - - + +
589B GLY 4.2 0.8 + - - -
590B LEU* 1.3 72.2 - - - +
592B HIS* 1.3 60.4 + - - +
593B PHE* 3.5 40.2 + - + -
605B ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 592 (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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382B DAH 4.0 0.2 - - - -
406B VAL* 3.8 19.7 - - + -
430B PHE* 3.9 1.6 - - - -
431B HIS* 3.0 39.1 + + + +
433B HIS* 4.3 5.4 - - + -
590B LEU* 3.9 3.5 - - + -
591B THR* 1.3 70.7 - - - +
593B PHE* 1.3 67.9 + - - +
594B PRO* 3.0 35.9 - - + +
595B ARG* 5.8 0.4 - - + -
598B ASP* 2.9 30.4 + - - -
602B MET* 4.0 17.3 - - + +
605B ASP* 5.8 4.5 - - - +
1002B CU 2.2 33.8 - - - -
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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