Contacts of the strand formed by residues 578 - 586 (chain B) in PDB entry 3F8I
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 LEU 578 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B SER 4.2 1.9 - - - +
503B ASP* 2.8 33.4 + - + +
504B GLN* 3.1 34.6 + - - +
570B PRO* 4.4 17.3 - - + -
571B GLU* 3.4 34.3 - - - +
572B ARG* 4.0 13.4 - - + +
576B GLY 4.0 0.2 + - - -
577B PHE* 1.3 73.4 - - - +
579B VAL* 1.3 67.8 + - - +
580B TRP* 5.3 4.0 - - + +
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASP* 3.9 28.0 - - - +
484B THR* 4.1 10.5 - - + -
500B GLN* 4.1 20.0 - - + +
504B GLN* 3.4 22.4 - - - +
570B PRO* 3.4 4.0 - - - +
571B GLU 2.8 37.3 + - - +
573B GLY* 4.1 9.6 - - - -
575B SER* 5.5 0.4 - - - +
577B PHE* 4.2 6.7 - - + +
578B LEU* 1.3 80.6 - - - +
580B TRP* 1.3 65.1 + - - +
581B ARG* 3.9 21.1 + - + +
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Residues in contact with TRP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B THR* 3.4 5.0 - - - +
485B GLY* 2.7 31.5 + - - +
504B GLN* 2.9 31.1 + - + +
505B LYS* 3.7 19.5 - - - +
506B LEU* 3.5 45.5 - - + +
510B ASN* 4.6 1.8 - - - +
523B GLU* 3.4 33.4 - - - -
525B GLY* 4.1 3.6 - - - -
568B TYR* 3.7 24.5 - + + -
569B TRP* 3.6 22.2 - - - -
570B PRO* 3.6 35.8 - - + +
578B LEU* 5.3 4.7 - - + +
579B VAL* 1.3 75.8 - - - +
581B ARG* 1.3 59.7 + - - +
582B TYR* 3.8 17.7 - - + +
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Residues in contact with ARG 581 (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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473B ASP* 2.8 37.2 + - - +
475B VAL* 3.7 18.8 - - - +
482B THR* 3.8 18.9 - - + +
483B TYR 3.2 7.8 + - - +
484B THR* 5.0 3.7 + - - +
568B TYR* 3.1 6.8 - - - +
569B TRP* 2.9 58.2 + - + +
571B GLU* 3.1 40.7 + - + -
579B VAL* 4.1 18.8 - - + +
580B TRP* 1.3 76.8 - - - +
582B TYR* 1.3 63.4 + - - +
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Residues in contact with TYR 582 (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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481B PHE 3.6 0.7 - - - +
482B THR* 3.1 8.9 - - - -
483B TYR* 2.8 43.7 + - + +
484B THR 4.5 0.4 - - - -
485B GLY* 3.9 14.4 - - - -
506B LEU* 4.0 3.6 - - + +
510B ASN* 2.8 37.7 + - - +
513B LEU* 3.7 30.7 - - + -
514B ALA* 3.8 23.3 - - + -
565B VAL* 4.5 10.8 - - + -
567B LYS 3.5 4.7 - - - +
568B TYR* 3.4 27.6 - + + -
569B TRP* 4.4 1.1 - - - -
580B TRP* 3.8 28.2 - + + +
581B ARG* 1.3 75.0 - - - +
583B LEU* 1.3 60.9 + - - +
584B LEU* 3.8 18.2 + - + +
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Residues in contact with LEU 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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480B TYR* 4.2 29.4 - - + -
481B PHE 3.7 14.6 - - - +
482B THR* 4.0 13.0 - - - +
565B VAL* 3.6 2.9 - - - -
566B VAL* 2.8 44.4 + - + +
567B LYS* 2.8 49.3 + - + +
569B TRP* 4.1 8.3 - - + -
582B TYR* 1.3 74.0 - - - +
584B LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 584 (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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465B LEU* 4.3 19.7 - - + -
480B TYR* 3.3 9.7 - - - +
481B PHE* 2.9 69.3 + - + +
483B TYR* 3.8 18.2 - - + -
513B LEU* 4.8 1.6 - - + -
537B VAL* 4.4 9.6 - - + -
539B VAL* 5.4 0.2 - - + -
563B TYR* 4.2 15.0 - - + -
564B LYS 3.3 12.6 - - - +
565B VAL* 3.7 24.7 - - + -
566B VAL* 4.7 0.4 - - - -
582B TYR* 3.9 16.6 - - + +
583B LEU* 1.3 76.9 - - - +
585B ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 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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479B ASN* 3.3 8.0 - - + +
480B TYR* 3.1 43.1 + - + -
531B TRP* 3.1 57.5 - - + +
563B TYR* 3.4 4.3 - - - -
564B LYS* 2.7 35.0 + - - +
566B VAL* 3.8 19.1 - - + -
584B LEU* 1.3 74.8 - - - +
586B ARG* 1.3 67.5 + - - +
587B ASP 3.6 0.5 + - - -
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Residues in contact with ARG 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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431B VAL* 3.8 15.8 - - - +
479B ASN* 2.9 35.9 + - - +
531B TRP* 4.0 5.7 - - - -
560B ASP 2.9 29.7 + - - -
561B GLY* 4.6 0.2 - - - -
562B ILE 3.6 8.3 - - - +
563B TYR* 3.2 35.5 + - + -
585B ARG* 1.3 82.3 + - - +
587B ASP* 1.3 61.9 + - - +
588B ASP* 3.7 26.5 + - - +
590B GLU 2.9 29.7 + - - -
591B PRO 3.9 3.6 + - - -
592B GLU* 3.7 30.6 + - - +
594B TRP* 4.6 1.0 - - - -
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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