Contacts of the strand formed by residues 573 - 579 (chain B) in PDB entry 3J0A
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 VAL 573 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551B GLU 4.0 2.8 + - - -
552B ILE* 3.7 22.7 - - + +
553B LEU 3.6 19.6 + - - -
571B LEU* 4.1 2.7 - - - +
572B SER* 1.3 85.2 - - - +
574B LEU* 1.3 64.6 + - - +
575B ASP* 4.0 6.3 + - + +
600B THR 5.8 0.2 - - - +
602B ALA 4.8 8.5 - - - +
603B GLY* 5.9 1.8 - - - -
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Residues in contact with LEU 574 (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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541B LEU* 6.1 0.7 - - + -
543B HIS* 5.8 3.8 - - + -
553B LEU* 3.5 42.6 - - + +
555B ILE* 4.3 10.3 - - + -
568B PHE* 6.4 0.2 - - + -
571B LEU* 3.6 25.8 - - + -
572B SER 3.6 2.6 + - - -
573B VAL* 1.3 73.3 - - - +
575B ASP* 1.3 76.5 + - - +
576B ILE* 3.5 18.5 + - + +
593B TRP* 5.8 10.3 - - + -
594B LEU* 5.9 3.8 - - + -
601B ILE* 4.5 13.2 - - + +
602B ALA* 3.2 11.6 + - - +
603B GLY* 3.1 23.8 + - - -
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Residues in contact with ASP 575 (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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553B LEU 3.6 5.9 + - - -
554B ASP* 2.8 33.6 - - + +
555B ILE* 2.7 46.5 + - - +
556B SER* 3.7 9.6 + - - -
573B VAL* 3.9 8.1 + - + +
574B LEU* 1.3 75.3 - - - +
576B ILE* 1.3 66.1 + - - +
577B THR* 3.3 23.1 + - - +
603B GLY* 4.5 5.4 - - - -
604B PRO* 4.8 7.2 - - + +
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Residues in contact with ILE 576 (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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541B LEU* 4.9 12.6 - - + -
555B ILE* 3.0 27.4 - - + -
560B LEU* 5.1 3.8 - - + -
574B LEU* 3.5 22.6 + - + +
575B ASP* 1.3 79.2 + - - +
577B THR* 1.3 61.0 + - - +
579B ASN* 3.4 13.1 + - - +
581B PHE* 3.5 34.6 - - + -
590B PHE* 5.3 3.1 - - + -
594B LEU* 4.6 26.0 - - + -
602B ALA* 5.1 4.7 - - + -
603B GLY* 4.3 10.9 - - - +
608B ILE* 3.5 20.7 - - + +
621B LEU* 5.7 0.6 - - + +
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Residues in contact with THR 577 (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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555B ILE 3.6 1.4 + - - -
556B SER* 3.4 17.0 - - - -
575B ASP* 3.3 18.5 + - - +
576B ILE* 1.3 80.2 - - - +
578B HIS* 1.3 74.8 + - - +
579B ASN* 3.0 10.6 + - - +
581B PHE* 5.1 0.2 - - - -
603B GLY 4.4 0.9 - - - -
604B PRO* 3.0 42.6 - - + +
607B ASP* 3.4 23.1 - - + +
608B ILE* 3.6 10.3 - - + -
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Residues in contact with HIS 578 (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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556B SER* 5.4 0.4 - - - -
557B ARG* 3.1 33.9 + - + +
558B ASN 3.8 0.5 + - - +
577B THR* 1.3 78.3 - - - +
579B ASN* 1.3 64.9 + - - +
580B LYS* 6.3 3.6 - - - -
581B PHE* 5.0 0.8 - - - -
607B ASP* 2.8 23.7 + - + +
608B ILE* 4.5 3.7 - - - +
609B TYR 5.7 1.8 - - - +
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Residues in contact with ASN 579 (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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555B ILE* 4.1 1.4 + - - -
556B SER* 3.5 4.9 - - - -
557B ARG 3.2 6.2 + - - -
558B ASN* 2.9 41.7 + - - +
560B LEU* 4.9 5.8 - - + +
576B ILE* 3.4 11.9 - - - +
577B THR 3.0 34.5 + - - +
578B HIS* 1.3 76.2 - - - +
580B LYS* 1.3 62.5 + - - +
581B PHE* 2.9 52.5 + - + -
609B TYR 4.0 5.3 + - - +
611B VAL* 3.8 12.4 - - - +
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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