Contacts of the strand formed by residues 570 - 578 (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 TYR 570 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B GLU* 4.0 18.7 + - - +
502B PHE* 3.9 27.3 - + + -
503B LYS* 3.8 35.1 - - + +
542B TRP* 6.0 0.2 - - - -
562B LEU* 3.9 28.8 - - + +
563B ILE 3.6 2.2 - - - -
564B LEU* 3.9 32.5 - - + +
568B LYS 4.6 4.9 - - - -
569B ILE* 1.3 83.2 - - - +
571B GLN* 1.3 59.7 + - - +
572B PRO* 3.5 10.4 - - - +
618B GLU* 6.0 0.5 - - - -
636B TYR* 3.9 36.8 + + - -
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Residues in contact with GLN 571 (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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538B LEU* 5.5 0.2 - - - +
562B LEU* 3.5 2.3 - - - -
563B ILE* 2.9 35.1 + - + +
565B GLU* 3.7 19.5 - - + +
569B ILE* 5.1 4.6 - - + +
570B TYR* 1.3 71.5 - - - +
572B PRO* 1.3 97.1 + - - +
573B SER* 3.2 4.7 + - - +
590B HIS* 3.6 44.8 - - + +
591B VAL 3.2 19.2 + - - -
592B LEU 4.6 0.6 + - - -
593B PRO* 4.2 16.6 - - - +
594B ASP 4.9 2.1 + - - -
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Residues in contact with PRO 572 (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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538B LEU* 3.6 28.7 - - + -
541B PHE* 3.7 27.1 - - + -
542B TRP* 4.2 12.6 - - + +
561B VAL 3.7 5.8 - - - +
562B LEU* 3.9 13.2 - - + -
570B TYR 3.5 10.5 - - - +
571B GLN* 1.3 100.8 + - - +
573B SER* 1.3 61.1 + - - +
591B VAL* 2.8 24.8 + - + -
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Residues in contact with SER 573 (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 PHE* 3.3 10.1 - - - -
560B PRO* 3.6 1.0 - - - +
561B VAL* 2.9 46.3 + - - +
563B ILE* 3.4 16.6 - - - +
571B GLN 3.2 8.7 + - - -
572B PRO* 1.3 77.8 + - - +
574B TYR* 1.3 67.9 + - - +
588B ILE* 5.0 0.4 - - - -
589B TRP 3.2 13.5 - - - -
590B HIS* 3.2 21.1 + - - -
591B VAL* 4.1 2.7 - - - +
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Residues in contact with TYR 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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540B ASP* 4.5 0.9 + - - +
541B PHE* 3.7 27.0 + + + -
544B ASP* 2.8 33.2 + - - +
558B ARG* 3.4 43.5 + - + +
559B PHE 3.3 16.8 - - - -
560B PRO* 3.6 15.0 - - + -
561B VAL* 4.5 1.8 - - - -
573B SER* 1.3 73.0 - - - +
575B LEU* 1.3 61.2 + - - +
588B ILE* 3.4 4.5 - - - +
589B TRP* 2.8 66.8 + - + -
591B VAL* 3.4 34.1 - - + -
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Residues in contact with LEU 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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558B ARG* 3.2 5.0 - - - -
559B PHE* 2.8 60.2 + - + +
561B VAL* 4.3 11.2 - - + -
574B TYR* 1.3 76.8 - - - +
576B SER* 1.3 65.5 + - - +
577B ILE* 4.4 3.4 - - + -
586B ILE* 4.5 5.4 - - + -
587B SER 3.2 9.4 - - - +
588B ILE* 4.1 18.6 - - + -
589B TRP* 4.8 1.8 - - - -
635B ILE* 3.9 25.1 - - + -
637B PHE* 4.6 2.7 - - + -
646B PHE* 3.4 48.0 - - + -
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Residues in contact with SER 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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557B VAL* 3.4 22.4 - - - -
558B ARG* 4.0 7.6 - - - -
559B PHE* 5.1 1.1 - - - -
575B LEU* 1.3 79.6 - - - +
577B ILE* 1.3 65.9 + - - +
578B ASN* 2.8 25.0 + - - -
585B THR 3.9 0.2 - - - +
586B ILE* 3.4 5.4 - - - +
587B SER* 2.8 47.7 + - - +
589B TRP* 4.1 9.6 - - - -
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Residues in contact with ILE 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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557B VAL* 4.5 7.2 + - - +
559B PHE* 5.0 5.5 - - + -
575B LEU* 4.4 3.1 - - + -
576B SER* 1.3 79.5 - - - +
578B ASN* 1.3 65.4 + - - +
579B ASN 4.2 0.9 + - - -
584B LYS* 5.6 1.3 - - + -
585B THR 3.6 5.8 - - - +
586B ILE* 4.0 17.3 - - + -
646B PHE* 3.8 33.9 - - + -
649B MET* 3.4 46.5 - - + +
650B VAL* 4.3 8.1 - - + -
653B ILE* 4.4 25.6 - - + -
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Residues in contact with ASN 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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576B SER* 2.8 24.3 + - - -
577B ILE* 1.3 75.4 - - - +
579B ASN* 1.3 59.2 + - - +
580B GLU* 3.0 17.8 + - + +
584B LYS* 3.6 9.5 - - - +
585B THR* 2.8 51.1 + - - +
587B SER* 2.8 33.7 + - - +
603B ASN* 4.1 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