Contacts of the strand formed by residues 572 - 579 (chain A) in PDB entry 5FMH
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 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A LEU* 3.2 6.0 - - - -
569A ARG* 2.8 39.6 + - + +
570A ASP* 5.0 2.5 - - + -
571A LYS* 1.3 78.4 - - - +
573A VAL* 1.3 77.5 + - - +
574A VAL* 3.1 10.2 + - + -
592A ILE 5.7 0.2 - - - +
595A GLY* 4.1 27.4 - - - +
596A GLU 4.3 2.5 - - - -
597A GLN* 3.4 33.9 - - - +
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Residues in contact with VAL 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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566A PHE* 4.1 10.1 - - + -
567A TYR 3.6 5.4 - - - +
568A LEU* 3.9 15.5 - - + -
571A LYS 4.1 1.2 + - - +
572A VAL* 1.3 80.1 - - - +
574A VAL* 1.3 57.9 + - - +
575A GLY 3.5 24.2 - - - +
576A ILE* 3.9 23.3 - - + -
591A ILE* 4.0 23.5 - - + +
592A ILE* 4.0 21.3 - - + +
595A GLY* 5.2 0.3 - - - -
596A GLU 4.6 3.2 + - - -
598A HIS* 4.4 11.4 - - + -
601A LEU* 3.9 22.9 - - + -
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Residues in contact with VAL 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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447A LEU* 4.6 8.5 - - + +
496A GLY* 3.6 6.2 - - - -
497A LEU* 2.9 31.6 + - + +
502A LEU* 4.2 9.2 - - + -
567A TYR 2.7 27.9 + - - +
568A LEU 4.0 1.3 - - - -
569A ARG* 3.5 51.4 - - + +
572A VAL* 3.1 12.7 + - + +
573A VAL* 1.3 77.0 - - - +
575A GLY* 1.3 54.3 + - - +
592A ILE* 4.0 14.4 - - - +
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Residues in contact with GLY 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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495A ILE 3.2 12.1 - - - -
497A LEU 3.2 17.0 - - - -
567A TYR* 2.9 32.5 + - - -
573A VAL* 3.5 4.3 - - - +
574A VAL* 1.3 79.3 - - - +
576A ILE* 1.3 69.9 + - - +
592A ILE* 3.8 4.3 - - - -
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Residues in contact with ILE 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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493A GLU 4.0 0.2 - - - +
494A ALA* 3.3 4.2 - - - -
495A ILE* 2.9 41.9 + - + +
498A VAL* 3.8 3.6 - - - +
564A VAL* 4.0 4.3 - - + -
565A ILE 3.2 7.0 - - - +
566A PHE* 3.8 29.2 - - + -
567A TYR* 4.3 0.4 - - - -
573A VAL* 3.9 14.4 - - + -
575A GLY* 1.3 79.9 - - - +
577A VAL* 1.3 76.8 + - - +
578A LEU* 3.9 20.4 - - + -
588A ALA* 3.9 37.2 - - + +
591A ILE* 4.2 7.2 - - + -
592A ILE* 4.0 2.7 - - + +
608A PHE* 4.2 6.1 - - + -
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Residues in contact with VAL 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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310A PHE* 6.1 1.8 - - + -
343A ILE* 4.6 4.7 - - + -
344A LEU* 3.8 25.8 - - + -
348A LEU* 4.9 3.6 - - + -
492A TYR* 4.9 8.5 - - + -
493A GLU 3.2 7.9 - - - +
494A ALA* 4.0 11.2 - - + -
498A VAL* 3.9 13.0 - - + -
563A GLY 4.0 0.3 - - - +
564A VAL* 3.4 4.3 - - - -
565A ILE* 2.8 47.9 + - + +
567A TYR* 3.6 30.9 - - + +
576A ILE* 1.3 78.3 - - - +
578A LEU* 1.3 71.9 + - - +
579A TRP 4.7 1.1 - - - +
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Residues in contact with LEU 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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492A TYR* 3.3 6.1 - - - +
493A GLU* 2.8 59.5 + - + +
563A GLY 3.6 1.1 - - - -
564A VAL* 3.8 26.9 - - + -
576A ILE* 3.9 9.6 - - + -
577A VAL* 1.3 75.6 - - - +
579A TRP* 1.3 60.3 + - - +
580A ASN 4.0 1.0 + - - -
581A ILE* 4.0 30.6 + - + +
584A ARG* 4.3 13.7 - - + -
585A MET* 4.5 10.1 - - + -
588A ALA* 4.8 3.1 - - + -
608A PHE* 3.6 38.4 - - + -
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Residues in contact with TRP 579 (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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347A TYR* 4.6 5.2 - + - -
348A LEU* 3.6 30.9 - - + +
351A TRP* 3.5 55.0 - + - -
490A VAL* 4.1 3.0 - - + +
491A GLY 3.6 13.9 - - - -
492A TYR* 3.7 20.0 - + + +
508A PHE* 3.7 37.9 - + + -
560A TYR* 3.5 26.2 - - + -
561A GLY* 3.8 9.9 - - - -
562A LYS* 3.2 22.1 - - - +
563A GLY 2.8 39.2 + - - +
565A ILE* 5.8 0.7 - - + -
577A VAL* 4.1 1.5 - - + -
578A LEU* 1.3 72.0 - - - +
580A ASN* 1.3 80.1 + - - +
581A ILE* 3.3 0.9 + - - +
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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