Contacts of the strand formed by residues 583 - 589 (chain A) in PDB entry 4KXW
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 THR 583 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A GLY 3.0 12.0 + - - +
555A ARG* 3.8 17.0 - - - +
556A ILE* 2.9 31.3 + - - +
581A GLY 3.9 6.6 + - - +
582A ILE* 1.3 79.8 - - - +
584A VAL* 1.3 67.3 + - - +
585A THR* 5.6 2.0 - - - -
619A LEU* 5.5 5.9 - - - +
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Residues in contact with VAL 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ILE* 3.4 16.2 - - + +
558A THR* 4.3 9.9 - - - +
569A GLY 4.7 2.5 - - - +
572A VAL* 4.2 17.7 - - + -
573A SER* 3.8 24.5 - - - +
576A VAL* 3.5 32.3 - - + -
582A ILE* 4.5 0.4 - - + -
583A THR* 1.3 79.1 - - - +
585A THR* 1.3 73.1 + - - +
586A HIS* 5.4 4.0 - - + +
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Residues in contact with THR 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ILE 2.9 11.9 + - - +
557A LEU* 3.3 19.9 - - + -
558A THR 2.9 24.8 + - - -
583A THR* 5.4 2.3 - - - -
584A VAL* 1.3 77.7 + - - +
586A HIS* 1.3 68.2 + - - +
587A LEU* 5.8 1.6 - - + -
615A ALA* 5.1 6.5 - - + +
619A LEU* 3.5 32.3 - - + +
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Residues in contact with HIS 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A THR 3.5 7.9 - - - -
560A GLU* 2.6 29.5 + - - -
564A TYR* 3.4 57.5 + + + -
569A GLY* 3.5 27.5 - - - -
570A GLU* 4.2 2.8 - - + +
573A SER* 5.8 1.3 + - - +
584A VAL* 5.4 4.0 - - + +
585A THR* 1.3 83.9 - - - +
587A LEU* 1.3 88.5 + - - +
588A ALA* 3.6 6.7 - - - +
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Residues in contact with LEU 587 (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 LEU* 4.1 15.0 - - + -
558A THR 2.7 12.2 + - - +
559A VAL* 3.3 12.1 - - + -
560A GLU 3.1 22.0 + - - -
564A TYR* 3.9 0.9 - - - -
585A THR* 5.9 2.0 - - + -
586A HIS* 1.3 81.6 - - - +
588A ALA* 1.3 61.2 + - - +
606A GLY 3.8 19.3 - - - +
607A ILE* 4.0 1.8 - - - -
611A ALA* 3.8 24.5 - - + +
612A ILE* 3.9 24.5 - - + -
615A ALA* 4.0 16.4 - - + -
1003A EDO 3.8 20.9 - - - +
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Residues in contact with ALA 588 (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 GLU* 3.5 15.0 - - + -
562A HIS 3.3 12.3 - - - +
564A TYR* 3.2 29.7 + - + -
586A HIS* 3.6 20.0 - - - +
587A LEU* 1.3 75.6 - - - +
589A VAL* 1.3 60.3 + - - +
605A PHE 3.3 11.3 - - - +
606A GLY 4.9 0.6 + - - +
607A ILE* 3.8 7.9 - - - +
1003A EDO 3.3 19.6 + - - -
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Residues in contact with VAL 589 (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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419A VAL* 4.2 6.5 - - + -
431A LEU* 4.1 5.4 - - + -
561A ASP* 3.9 21.3 - - - +
562A HIS 3.0 20.3 + - - +
563A TYR* 3.3 30.7 - - + +
564A TYR* 3.5 6.3 + - - -
588A ALA* 1.3 76.1 - - - +
590A ASN* 1.4 59.3 + - - +
591A ARG 3.5 21.8 - - - +
593A PRO* 3.9 18.6 - - + -
605A PHE* 4.1 19.7 - - + -
607A ILE* 3.9 16.2 - - + -
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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