Contacts of the strand formed by residues 570 - 578 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A GLU* 4.0 17.9 + - + +
502A PHE* 3.8 28.3 - + + -
503A LYS* 3.8 35.6 - - + +
542A TRP* 5.9 0.3 - - - -
562A LEU* 3.9 28.0 - - + +
563A ILE 3.6 2.5 - - - -
564A LEU* 3.9 33.6 - - + +
568A LYS 4.6 4.5 - - - -
569A ILE* 1.3 81.7 - - - +
571A GLN* 1.3 59.7 + - - +
572A PRO* 3.5 10.4 - - - +
618A GLU* 6.0 0.3 - - - -
636A TYR* 3.9 36.1 + + - -
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Residues in contact with GLN 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A LEU* 5.5 0.2 - - - +
562A LEU* 3.5 2.7 - - - -
563A ILE* 2.9 37.4 + - + +
565A GLU* 3.7 19.9 - - + +
569A ILE* 3.7 5.5 + - + +
570A TYR* 1.3 70.4 - - - +
572A PRO* 1.3 95.7 + - - +
573A SER* 3.2 4.6 + - - +
590A HIS* 3.6 43.5 - - + +
591A VAL 3.2 19.4 + - - -
592A LEU 4.6 0.6 + - - -
593A PRO* 4.2 16.4 - - - +
594A ASP 4.9 2.1 + - - -
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Residues in contact with PRO 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A LEU* 3.6 29.2 - - + -
541A PHE* 3.7 26.2 - - + -
542A TRP* 4.1 12.8 - - + +
561A VAL 3.7 6.1 - - - +
562A LEU* 3.8 12.8 - - + -
570A TYR 3.5 10.3 - - - +
571A GLN* 1.3 101.2 + - - +
573A SER* 1.3 60.5 + - - +
591A VAL* 2.8 23.7 + - + -
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Residues in contact with SER 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A PHE* 3.3 9.7 - - - -
560A PRO* 3.6 0.9 - - - +
561A VAL* 2.9 46.8 + - - +
563A ILE* 3.4 16.7 - - - +
571A GLN 3.2 9.0 + - - -
572A PRO* 1.3 78.2 + - - +
574A TYR* 1.3 68.3 + - - +
588A ILE* 5.0 0.2 - - - -
589A TRP 3.1 13.7 - - - -
590A HIS* 3.2 21.0 + - - -
591A VAL* 4.1 2.9 - - - +
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Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A ASP* 4.5 1.0 + - - +
541A PHE* 3.7 26.4 + + + -
544A ASP* 2.8 32.5 + - - +
558A ARG* 3.4 43.9 + - + -
559A PHE 3.3 16.6 - - - -
560A PRO* 3.7 15.5 - - + -
561A VAL* 4.5 1.3 - - - -
573A SER* 1.3 73.7 - - - +
575A LEU* 1.3 60.6 - - - +
588A ILE* 3.4 5.4 - - - +
589A TRP* 2.8 66.7 + - + -
591A VAL* 3.5 32.8 - - + -
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A ARG* 3.2 5.7 - - - -
559A PHE* 2.8 59.3 + - + +
561A VAL* 4.3 10.8 - - + -
574A TYR* 1.3 75.5 - - - +
576A SER* 1.3 67.1 + - - +
577A ILE* 4.4 3.4 - - + -
586A ILE* 4.5 4.9 - - + -
587A SER 3.2 9.4 - - - +
588A ILE* 4.1 18.6 - - + -
589A TRP* 4.8 2.0 - - - -
635A ILE* 4.0 27.1 - - + -
637A PHE* 4.6 2.2 - - + -
646A PHE* 3.4 48.5 - - + -
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Residues in contact with SER 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A VAL* 3.5 22.9 - - - -
558A ARG* 4.0 8.1 - - - +
559A PHE* 5.1 1.1 - - - -
575A LEU* 1.3 79.5 - - - +
577A ILE* 1.3 66.8 + - - +
578A ASN* 2.8 24.0 + - - -
585A THR 3.9 0.3 - - - +
586A ILE* 3.4 5.9 - - - +
587A SER* 2.8 47.2 + - - +
589A TRP* 4.1 9.6 - - - -
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Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A VAL 4.5 6.5 + - - +
559A PHE* 5.0 3.3 - - + -
575A LEU* 4.4 3.1 - - + -
576A SER* 1.3 80.1 - - - +
578A ASN* 1.3 64.7 + - - +
579A ASN 4.1 0.7 + - - -
584A LYS* 5.7 1.3 - - + -
585A THR 3.6 6.3 - - - +
586A ILE* 4.0 17.0 - - + -
646A PHE* 3.8 30.3 - - + -
649A MET* 4.0 41.7 - - + -
650A VAL* 4.3 8.1 - - + -
653A ILE* 4.4 25.6 - - + -
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Residues in contact with ASN 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A SER* 2.8 23.5 + - - -
577A ILE* 1.3 75.4 - - - +
579A ASN* 1.3 58.6 + - - +
580A GLU* 2.9 18.2 + - + +
584A LYS* 3.6 9.2 - - - +
585A THR* 2.8 51.6 + - - +
587A SER* 2.8 34.2 + - - +
603A ASN* 4.1 0.8 - - - +
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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