Contacts of the strand formed by residues 556 - 566 (chain A) in PDB entry 3E20
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 ALA 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A MET* 4.2 14.6 - - + +
503A PRO* 3.7 29.8 - - + -
554A VAL 3.8 0.8 + - - -
555A HIS* 1.3 77.4 - - - +
557A THR* 1.3 66.4 + - - +
628A PRO* 4.6 4.3 - - + -
629A VAL 3.5 12.3 - - - +
630A CYS* 3.9 7.4 - - - -
631A MET 4.6 0.7 - - - +
662A ASP* 3.4 12.3 - - - +
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Residues in contact with THR 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ALA* 1.3 79.2 - - - +
558A THR* 1.3 68.1 + - - +
559A ARG 2.9 28.5 + - - +
625A THR* 3.8 2.8 + - - +
628A PRO* 3.6 5.5 - - - +
629A VAL* 3.2 27.0 + - - +
631A MET* 4.0 17.2 - - + +
660A ILE* 3.8 28.5 - - + -
661A LEU 3.1 15.8 + - - -
662A ASP* 3.4 15.1 + - - -
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Residues in contact with THR 558 (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 THR* 1.3 73.9 + - - +
559A ARG* 1.3 69.5 + - - +
560A PHE* 5.0 3.4 - - - -
623A LEU 3.5 0.7 - - - +
624A GLU* 3.0 9.9 - - - +
625A THR* 2.9 57.1 + - - +
626A GLN 4.3 2.9 - - - +
627A THR* 3.5 3.8 - - - -
628A PRO* 3.5 31.4 - - + -
662A ASP* 5.5 0.2 + - - -
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Residues in contact with ARG 559 (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 THR* 2.9 17.3 + - - +
558A THR* 1.3 89.0 + - - +
560A PHE* 1.3 64.7 + - - +
594A LYS* 4.9 3.2 - - - +
622A GLU* 2.8 31.7 + - - +
623A LEU 3.3 2.5 - - - +
624A GLU* 3.7 37.3 + - + +
661A LEU* 3.1 39.3 + - + +
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Residues in contact with PHE 560 (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 THR* 4.3 3.6 - - + -
558A THR 4.9 1.8 - - - -
559A ARG* 1.3 79.4 - - - +
561A ILE* 1.3 73.5 + - - +
562A ALA* 3.9 13.9 - - + -
581A MET* 2.9 37.5 - - + -
590A VAL* 4.5 5.8 - - + -
622A GLU* 3.5 2.5 - - - +
623A LEU* 2.7 78.1 + - + +
625A THR* 4.6 6.5 - - + -
631A MET* 3.6 38.6 - - + -
643A PHE* 4.0 6.5 - + - -
657A VAL* 4.1 6.7 - - + -
659A LYS 3.4 16.6 - - - +
660A ILE* 4.4 1.6 - - + -
661A LEU* 4.0 5.7 - - - +
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Residues in contact with ILE 561 (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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560A PHE* 1.3 77.4 - - - +
562A ALA* 1.3 60.4 + - - +
596A LEU* 3.8 30.5 - - + -
620A ILE* 3.8 13.2 - - + -
621A ALA 3.2 13.7 - - - +
622A GLU* 4.4 7.2 - - + +
657A VAL* 3.7 2.3 - - - +
658A VAL* 2.7 46.1 + - + +
659A LYS* 3.0 22.3 + - + +
661A LEU* 4.2 28.5 - - + -
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Residues in contact with ALA 562 (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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560A PHE* 3.9 9.6 + - + -
561A ILE* 1.3 77.9 - - - +
563A GLN* 1.3 63.1 + - - +
564A ILE* 3.5 8.6 - - + +
620A ILE* 4.4 2.7 - - - -
621A ALA 3.1 30.4 + - - +
623A LEU* 4.9 3.4 - - + -
643A PHE* 3.8 21.3 - - + -
656A LYS 3.0 24.7 - - - +
657A VAL* 3.7 3.8 - - - -
658A VAL* 3.6 5.4 - - - -
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Residues in contact with GLN 563 (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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562A ALA* 1.3 71.6 - - - +
564A ILE* 1.3 65.6 + - - +
565A ALA 4.3 0.2 - - - -
599A LEU* 3.9 20.2 - - + +
603A ASN* 3.5 28.1 + - - +
618A LYS* 6.4 0.6 - - - +
619A ILE 3.6 4.3 - - - -
620A ILE* 4.3 15.5 - - + +
655A GLY* 3.1 1.4 - - - -
656A LYS* 3.0 60.8 + - + +
658A VAL* 4.2 10.7 - - + +
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Residues in contact with ILE 564 (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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562A ALA 3.5 12.3 - - - +
563A GLN* 1.3 82.3 - - - +
565A ALA* 1.3 62.0 + - - +
566A ILE* 3.4 11.7 + - + +
592A PHE* 3.6 33.7 - - + -
599A LEU* 5.7 0.2 - - - +
618A LYS* 4.7 1.6 - - - -
619A ILE* 2.7 45.4 + - + +
621A ALA* 4.7 5.2 - - + -
623A LEU* 3.9 24.5 - - + -
643A PHE* 4.5 9.0 - - + -
645A LEU* 4.5 7.9 - - + -
653A ALA* 3.7 21.8 - - + -
654A VAL 3.5 12.6 - - - +
655A GLY* 4.1 0.2 - - - -
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Residues in contact with ALA 565 (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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563A GLN 4.3 0.2 - - - -
564A ILE* 1.3 71.4 - - - +
566A ILE* 1.3 62.0 + - - +
567A LEU* 3.2 9.9 - - + +
617A MET 4.0 4.3 - - - -
618A LYS* 4.6 15.5 - - + +
653A ALA* 3.1 17.4 - - - +
654A VAL* 3.0 30.9 + - + +
655A GLY* 4.7 0.6 - - - -
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Residues in contact with ILE 566 (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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564A ILE* 3.4 14.4 - - + +
565A ALA* 1.3 72.7 - - - +
567A LEU* 1.3 66.0 + - - +
569A LEU* 3.8 20.2 - - + -
573A LEU* 5.1 11.7 - - + -
592A PHE* 6.1 2.2 - - + -
613A ALA* 4.7 11.4 - - + -
614A THR 3.3 28.7 - - - +
615A LYS* 3.4 14.6 - - - +
616A GLY* 2.8 27.9 + - - -
617A MET* 3.2 11.0 + - + +
619A ILE* 3.1 37.0 - - + -
652A VAL 3.8 3.6 - - - +
653A ALA* 3.9 6.3 - - + -
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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