Contacts of the strand formed by residues 22 - 35 (chain B) in PDB entry 3RTR
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 PHE 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A GLU* 4.8 3.1 - - - +
590A LEU* 4.5 11.9 - - + -
591A VAL 3.6 4.7 - - - -
592A THR* 3.6 31.0 - - + -
594A CYS* 4.2 17.0 - - - -
595A PHE* 4.4 12.8 - + - -
601A LEU* 3.9 18.4 - - + -
611A LEU* 3.3 49.8 - - + -
612A LEU* 3.5 24.5 - - + +
614A TYR* 4.1 14.4 - - + -
615A ASN* 2.7 29.2 + - - +
648A LEU* 5.5 1.1 - - + -
671A LEU* 4.6 9.6 - - + -
21B ARG* 1.3 77.3 - - - +
23B GLU* 1.3 65.3 + - - +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A GLU* 6.0 0.9 - - - -
590A LEU* 3.3 6.1 - - - +
591A VAL* 2.8 53.0 + - + +
593A ASN* 3.1 27.8 + - - +
612A LEU* 4.9 0.2 - - - -
21B ARG* 3.6 23.7 + - + +
22B PHE* 1.3 78.9 - - - +
24B VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ASP 4.3 4.5 - - - +
533A LEU* 3.4 44.3 - - + +
558A GLU* 3.8 32.3 - - + +
559A LEU* 4.1 4.9 - - + -
590A LEU* 3.5 21.3 - - + -
591A VAL* 5.5 0.7 - - - -
608A MET* 3.5 25.8 - - + -
612A LEU* 4.0 7.6 - - + -
23B GLU* 1.3 73.8 - - - +
25B LYS* 1.3 59.7 + - - +
26B LYS 4.0 11.2 - - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 3.5 2.9 - - - +
534A ASP* 2.7 38.1 + - + +
589A GLU* 3.0 21.7 + - + +
590A LEU 5.4 0.4 - - - -
591A VAL* 5.3 12.8 - - + -
600A THR* 5.0 14.1 + - + +
23B GLU 3.8 2.1 + - - +
24B VAL* 1.3 72.6 - - - +
26B LYS* 1.3 80.2 + - + +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 5.4 0.4 - - - -
534A ASP* 3.2 35.0 - - + +
588A GLY* 3.1 3.6 - - - -
589A GLU* 2.9 63.2 + - + +
608A MET* 4.3 0.3 - - - +
24B VAL* 4.0 8.9 - - - +
25B LYS* 1.3 102.6 - - + +
27B TRP* 1.3 63.8 + - - +
28B ASN* 5.2 11.0 - - - +
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Residues in contact with TRP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 4.6 8.3 - - + -
534A ASP 3.1 8.3 + - - +
535A PHE* 3.7 33.1 - + + -
536A SER 3.0 25.5 + - - +
555A LEU* 4.0 19.3 - - + -
559A LEU* 3.6 55.1 - - + +
562A SER* 4.3 6.5 - - - -
563A TYR* 4.7 2.9 - - + -
581A TRP* 4.0 22.7 - + - -
583A TYR* 4.4 18.4 - + - -
586A SER* 3.7 11.6 - - - -
587A LYS 3.3 20.4 - - - -
588A GLY* 4.2 4.0 - - - -
605A THR* 2.8 28.1 + - + +
608A MET* 4.5 4.3 - - - -
24B VAL* 5.0 0.4 - - + -
26B LYS* 1.3 76.5 - - - +
28B ASN* 1.3 64.5 + - - +
29B ALA* 3.8 5.7 + - + -
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A ASP 5.4 0.5 - - - +
536A SER* 2.9 24.3 + - - +
538A GLN* 4.3 14.4 - - - +
585A LEU 4.2 2.9 - - - +
586A SER* 3.4 21.1 - - - -
587A LYS* 2.8 47.2 + - + +
588A GLY* 5.3 2.2 - - - -
589A GLU* 6.1 1.8 - - - +
26B LYS* 5.2 10.1 - - - +
27B TRP* 1.3 80.2 + - - +
29B ALA* 1.3 64.8 + - - +
30B VAL* 4.3 1.9 - - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A PHE* 4.2 7.9 - - + -
536A SER 2.9 6.9 + - - -
537A ILE* 3.4 23.9 - - + -
538A GLN* 3.0 24.4 + - - +
581A TRP* 3.6 24.5 - - + -
586A SER* 3.4 12.8 - - - +
27B TRP* 3.8 9.8 - - + -
28B ASN* 1.3 73.6 - - - +
30B VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A VAL* 3.3 35.2 - - + +
538A GLN* 3.6 13.5 - - - +
540A LEU* 4.2 16.8 - - + -
581A TRP* 3.9 1.8 - - - +
582A LEU* 2.8 49.2 + - + +
585A LEU* 3.7 35.2 - - + +
586A SER* 3.5 3.9 + - - -
28B ASN 4.3 1.6 - - - +
29B ALA* 1.3 84.5 - - - +
31B ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ILE* 4.4 14.1 - - + +
538A GLN 3.4 6.7 + - - +
539A VAL* 3.4 4.2 - - + +
540A LEU* 2.9 27.4 + - - +
579A LEU* 3.3 23.3 - - + -
580A THR 3.0 17.9 - - - +
581A TRP* 3.9 12.8 - - + -
582A LEU* 4.3 0.9 - - - +
29B ALA 4.4 0.4 - - - -
30B VAL* 1.3 76.7 - - - +
32B LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 3.1 32.8 - - + +
541A SER 4.6 3.8 - - - -
542A SER* 4.2 26.2 - - - +
545A TRP* 4.5 21.5 - - + +
547A PHE* 4.6 18.2 - - + +
548A GLN* 5.9 0.9 - - - -
549A GLN* 5.6 7.9 - - - +
578A LYS 3.9 0.3 - - - +
579A LEU* 3.7 3.2 - - - -
580A THR* 2.7 48.2 + - - +
582A LEU* 4.0 29.4 - - + -
31B ALA* 1.3 72.8 - - - +
33B TRP* 1.3 61.3 + - - +
34B ALA* 5.4 0.5 - - - +
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Residues in contact with TRP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A ASP* 4.5 6.1 + - - -
513A VAL* 6.1 2.6 - - - +
539A VAL* 3.4 27.3 + - + -
540A LEU* 2.9 24.1 + - - -
541A SER* 3.6 20.7 - - - +
542A SER* 2.9 24.7 + - - -
570A TYR* 3.3 23.1 - - + +
577A ARG* 3.4 50.9 - - + +
578A LYS 3.5 9.6 - - - +
579A LEU* 4.0 4.5 - - + +
31B ALA 4.0 0.6 + - - -
32B LEU* 1.3 74.3 - - - +
34B ALA* 1.3 79.2 + - - +
35B TRP* 4.1 23.6 - + - -
50D MET* 3.7 27.2 - - + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A SER* 3.6 18.6 - - - +
577A ARG* 4.6 0.4 - - - -
578A LYS* 3.0 41.0 + - - +
32B LEU 4.1 0.4 + - - +
33B TRP* 1.3 86.4 - - - +
35B TRP* 1.3 71.6 + - - +
40D ASP* 4.6 8.3 - - - +
48D HIS* 4.8 1.3 - - + +
49D ILE* 6.4 0.2 - - + -
50D MET* 3.7 18.4 - - + -
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Residues in contact with TRP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A HIS* 5.8 0.9 - - + -
576A GLY* 3.6 19.7 - - - -
577A ARG* 3.8 29.6 - - + -
578A LYS* 4.1 10.9 + - - -
33B TRP* 4.1 22.2 - + - -
34B ALA* 1.3 77.5 - - - +
36B ASP* 1.3 61.0 + - - +
37B ILE* 3.7 19.1 + - + +
39D VAL 4.9 0.7 - - - +
40D ASP* 5.8 1.4 - - - -
49D ILE* 3.4 30.4 + - + +
50D MET* 3.7 17.6 - - - +
70D VAL* 4.0 24.0 - - + +
72D TRP* 3.7 37.7 - + + -
78D ALA* 5.4 0.2 - - + -
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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