Contacts of the strand formed by residues 585 - 590 (chain B) in PDB entry 5ULM
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 THR 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ILE* 3.6 5.9 - - - +
578B ASN* 2.8 57.4 + - - +
580B GLU* 4.2 14.7 + - + +
583B GLU* 3.7 10.8 - - + +
584B LYS* 1.3 82.4 - - - +
586B ILE* 1.3 63.5 + - - +
603B ASN* 3.9 22.0 + - - +
604B PHE 3.2 13.2 - - - +
605B SER* 4.0 11.4 - - - +
606B ALA 4.7 0.7 - - - +
653B ILE* 5.2 1.3 - - - -
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Residues in contact with ILE 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 4.5 8.7 - - + -
576B SER 3.4 8.5 - - - +
577B ILE* 4.0 12.1 - - + -
585B THR* 1.3 75.9 - - - +
587B SER* 1.3 64.8 + - - +
588B ILE* 3.9 25.1 - - + -
602B TRP 4.0 0.2 - - - +
603B ASN* 3.3 4.4 + - - -
604B PHE* 2.7 48.4 + - + +
606B ALA* 6.5 0.2 - - - -
609B VAL* 4.1 19.3 - - + -
624B LEU* 4.2 16.2 - - + -
646B PHE* 4.8 0.7 - - + -
650B VAL* 3.9 30.5 - - + -
653B ILE* 4.0 20.0 - - + -
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Residues in contact with SER 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 3.2 5.2 - - - +
576B SER* 2.8 42.5 + - - +
578B ASN* 2.8 20.9 + - - +
586B ILE* 1.3 69.5 - - - +
588B ILE* 1.3 64.6 + - - +
589B TRP* 4.1 14.6 - - - -
602B TRP 3.5 5.8 - - - -
603B ASN* 2.4 28.8 + - - -
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Residues in contact with ILE 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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561B VAL* 5.8 0.9 - - + -
563B ILE* 3.6 30.5 - - + -
573B SER* 5.0 1.8 - - - -
574B TYR 3.4 7.6 - - - +
575B LEU* 4.1 18.8 - - + -
586B ILE* 3.9 11.7 - - + -
587B SER* 1.3 80.8 - - - +
589B TRP* 1.3 67.5 + - - +
601B GLU* 3.5 1.9 - - - +
602B TRP* 2.9 48.8 + - + +
604B PHE* 4.3 14.1 - - + -
624B LEU* 3.8 28.9 - - + -
633B PHE* 4.3 12.6 - - + -
635B ILE* 4.4 4.5 - - + -
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Residues in contact with TRP 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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558B ARG* 3.5 31.8 - - + +
573B SER* 3.2 4.0 - - - -
574B TYR* 2.8 81.1 + + + +
575B LEU 5.0 0.4 - - - -
576B SER* 4.1 12.8 - - - -
587B SER* 4.1 21.5 - - - -
588B ILE* 1.3 85.4 - - - +
590B HIS* 1.3 75.6 + - - +
591B VAL* 3.7 2.5 + - + +
600B HIS 3.4 9.9 - - - +
601B GLU* 3.8 27.1 - - + +
602B TRP* 5.1 0.2 - - - -
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Residues in contact with HIS 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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563B ILE* 3.8 14.1 - - + +
565B GLU* 3.6 19.6 + - - -
571B GLN* 3.6 31.9 - - + +
572B PRO 3.6 4.3 - - - -
573B SER* 3.2 9.9 + - - -
589B TRP* 1.3 84.1 - - - +
591B VAL* 1.3 62.4 + - - +
592B LEU 3.8 1.6 + - - -
593B PRO* 4.3 12.5 - - + +
599B ILE 4.6 0.4 + - - -
600B HIS* 2.9 51.0 + + + +
602B TRP* 3.5 31.1 - + - -
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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