Contacts of the strand formed by residues 593 - 599 (chain A) in PDB entry 1L8A
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 ILE 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A LEU* 4.9 3.6 - - + -
511A ILE* 4.0 32.3 - - + -
514A ARG* 2.8 17.7 + - + -
515A LEU* 3.4 14.3 - - + -
516A VAL* 2.9 22.0 + - - -
591A PRO 5.3 0.9 - - - +
592A MET* 1.3 77.0 - - - +
594A PRO* 1.3 61.5 - - + +
595A PHE* 3.5 28.9 - - + -
621A GLY* 5.2 0.4 - - - -
622A PHE* 4.1 13.5 - - + -
674A LEU* 4.0 24.9 - - + -
678A TYR* 3.6 35.9 - - + -
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Residues in contact with PRO 594 (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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516A VAL* 3.2 13.5 - - + +
518A ILE* 4.1 5.2 - - + -
578A TRP* 3.4 40.6 - - + +
581A ALA* 3.7 15.7 - - + -
582A ALA* 3.6 14.4 - - + +
592A MET 3.4 11.9 - - - +
593A ILE* 1.3 86.9 - - - +
595A PHE* 1.3 63.8 + - - +
596A TYR 4.0 0.9 - - - -
620A ARG 3.9 13.9 - - - +
621A GLY* 3.9 2.6 - - - -
622A PHE* 2.9 29.6 + - - +
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Residues in contact with PHE 595 (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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498A PHE* 3.8 32.6 - + + -
502A LEU* 4.1 18.4 - - + -
505A MET* 3.5 29.4 - - - -
515A LEU* 4.3 8.1 - - + -
516A VAL 2.9 13.4 + - - +
517A PRO* 3.3 6.3 - - + +
518A ILE* 2.7 30.3 + - - +
519A ILE* 5.4 0.2 - - - +
593A ILE* 3.5 30.7 - - + -
594A PRO* 1.3 71.1 - - - +
596A TYR* 1.3 57.0 + - - +
597A ILE* 3.8 2.9 + - - +
622A PHE* 3.2 50.9 - + + -
624A ILE* 4.7 2.0 - - + -
670A MET* 3.8 19.3 - - + -
674A LEU* 5.1 0.2 - - + -
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Residues in contact with TYR 596 (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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518A ILE* 3.4 29.8 - - + -
520A ALA* 3.9 11.2 - - + +
571A GLU* 3.4 39.6 - - - +
574A ALA* 3.4 22.0 - - + +
575A GLY* 4.0 19.3 - - - -
578A TRP* 3.6 19.9 - - + -
595A PHE* 1.3 73.3 - - - +
597A ILE* 1.3 63.6 - - - +
598A TYR* 3.4 43.6 - + + +
602A PHE 5.1 0.6 + - - -
607A ILE* 4.5 9.2 - - + -
622A PHE 3.2 7.4 + - - +
623A LEU* 3.9 13.9 - - + -
624A ILE* 2.8 29.3 + - - +
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Residues in contact with ILE 597 (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 THR* 3.9 13.2 - - + -
498A PHE* 3.7 24.2 - - + -
518A ILE 3.1 9.0 + - - +
519A ILE* 3.7 35.2 - - + +
520A ALA 4.4 1.9 + - - -
522A GLU 5.0 0.2 - - - +
526A PHE* 3.9 35.7 - - + -
528A MET* 4.0 18.2 - - + -
595A PHE 3.8 1.1 + - - +
596A TYR* 1.3 78.2 - - - +
598A TYR* 1.3 67.8 + - - +
624A ILE* 3.3 35.2 - - + +
626A GLY 4.3 2.2 - - - +
691A THR* 4.2 2.9 - - - +
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Residues in contact with TYR 598 (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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520A ALA* 5.0 5.6 - - + -
526A PHE* 3.5 16.4 - - - -
571A GLU* 4.9 6.3 - - + +
596A TYR* 3.4 56.8 - + + +
597A ILE* 1.3 81.3 - - - +
599A TYR* 1.3 81.2 + - - +
600A SER* 3.1 10.7 + - - -
602A PHE* 4.2 5.2 - - + -
603A GLY* 3.4 34.8 - - - -
604A PHE* 4.5 3.6 - - - -
607A ILE* 6.0 0.7 - - + -
623A LEU* 4.1 13.1 - - + +
624A ILE 3.2 17.9 + - - -
625A GLY* 4.1 0.9 - - - -
626A GLY* 2.8 29.1 + - - -
688A TYR* 3.5 26.3 + - - -
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Residues in contact with TYR 599 (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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522A GLU* 2.7 43.4 + - + -
525A THR* 3.8 11.2 + - + +
526A PHE* 4.0 10.5 - + - -
571A GLU* 5.6 0.8 + - - -
598A TYR* 1.3 80.9 - - - +
600A SER* 1.3 65.9 + - - +
601A MET* 3.1 4.7 - - + +
602A PHE* 2.8 47.2 + + + +
627A THR* 3.1 32.8 - - + -
633A LEU* 4.0 23.6 - - + -
636A GLU* 5.2 5.1 + - + -
640A HIS* 4.2 16.6 - + - +
887A TPP 3.9 17.0 - + - -
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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