Contacts of the helix formed by residues 556 - 574 (chain A) 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 PRO 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553A PHE* 3.4 14.8 - - + -
554A ALA 2.8 8.0 - - - +
555A LEU* 1.3 87.8 - - + +
557A SER* 1.3 66.8 + - - +
558A GLU* 4.0 2.5 - - - +
559A LEU* 3.0 37.1 + - + -
560A GLU* 3.2 7.6 + - - +
609A ALA* 3.7 31.0 - - + +
612A LEU* 3.9 24.0 - - + -
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Residues in contact with SER 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU 3.8 1.2 + - - -
556A PRO* 1.3 72.1 - - - +
558A GLU* 1.3 70.7 + - - +
560A GLU* 3.4 29.6 + - - +
561A ARG* 4.2 6.4 + - - +
561C ARG* 4.3 8.1 + - - -
565C ARG* 3.7 24.3 + - - +
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Residues in contact with GLU 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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532A ASP* 3.3 25.8 - - - +
533A LEU* 3.9 5.5 - - + +
556A PRO* 3.0 1.8 + - - +
557A SER* 1.3 89.3 + - - +
559A LEU* 1.3 62.1 + - + +
560A GLU 3.7 0.3 + - - -
561A ARG* 4.3 4.0 + - - +
562A SER* 4.8 0.9 + - - -
612A LEU* 3.3 36.2 - - + +
615A ASN* 4.2 10.2 + - - -
22B PHE 4.8 2.1 - - - +
23B GLU* 6.0 0.4 - - - -
24B VAL* 3.8 34.3 - - + +
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Residues in contact with LEU 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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533A LEU* 4.0 17.9 - - + -
555A LEU* 3.6 15.5 - - + -
556A PRO* 3.0 33.6 + - + +
558A GLU* 1.3 76.5 - - + +
560A GLU* 1.3 65.6 + - - +
561A ARG 3.3 2.7 - - - -
562A SER* 3.1 9.6 + - - +
563A TYR* 2.9 21.5 + - - +
605A THR* 4.8 9.4 - - + +
608A MET* 4.3 14.6 - - + -
612A LEU* 5.5 1.3 - - + -
24B VAL* 4.1 13.0 - - + -
27B TRP* 3.6 51.9 - - + +
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Residues in contact with GLU 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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555A LEU* 3.7 29.8 - - + +
556A PRO 3.2 16.7 + - - +
557A SER* 3.5 24.3 + - - +
558A GLU 3.4 1.2 - - - -
559A LEU* 1.3 76.2 - - - +
561A ARG* 1.3 65.0 + - + +
563A TYR* 3.0 3.1 + - - +
564A GLN* 3.0 27.6 + - - +
561C ARG* 4.7 8.0 + - - +
564C GLN* 3.0 28.0 - - - +
565C ARG* 3.9 39.7 + - - +
568C ALA* 5.6 4.3 - - - +
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Residues in contact with ARG 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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530A PRO* 2.8 34.8 + - - +
531A LEU* 4.1 3.0 - - + +
532A ASP* 3.7 42.7 + - - +
557A SER 4.2 6.7 + - - +
558A GLU 4.3 2.0 + - - +
559A LEU 3.3 0.8 - - - -
560A GLU* 1.3 80.1 - - + +
562A SER* 1.3 64.2 + - - +
564A GLN* 3.8 18.1 - - - +
565A ARG* 3.2 52.9 + - - +
561C ARG* 6.4 1.8 - - + -
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Residues in contact with SER 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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521A PHE* 5.2 0.7 - - - -
531A LEU* 3.9 19.2 - - - +
532A ASP* 4.2 1.8 + - - -
533A LEU* 3.2 31.0 - - - +
535A PHE* 3.8 33.7 - - - +
558A GLU 4.8 0.5 + - - -
559A LEU* 3.1 11.2 + - - -
561A ARG* 1.3 78.7 - - - +
563A TYR* 1.3 66.4 + - - +
565A ARG* 4.3 1.6 - - - +
566A PHE* 3.4 21.3 + - - +
27B TRP* 4.3 7.4 - - - -
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Residues in contact with TYR 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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555A LEU* 3.4 25.6 - - + -
559A LEU 2.9 7.6 + - - +
560A GLU 3.3 7.0 - - - +
562A SER* 1.3 80.4 - - - +
564A GLN* 1.3 67.7 + - - +
566A PHE* 3.1 1.9 + - - +
567A THR* 2.8 41.9 + - + +
579A LEU 5.6 0.3 + - - -
581A TRP* 3.1 67.2 + + + -
583A TYR* 3.5 16.1 + - - -
27B TRP* 4.7 1.3 - - + -
564C GLN* 3.6 18.6 - - + -
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Residues in contact with GLN 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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560A GLU* 3.0 9.2 + - - +
561A ARG* 3.8 25.1 - - - +
563A TYR* 1.3 84.8 - - + +
565A ARG* 1.3 66.4 + - + +
567A THR* 3.5 5.8 + - - -
568A ALA* 3.2 17.2 + - - +
560C GLU* 2.8 63.2 + - + +
561C ARG* 4.2 18.0 - - - +
563C TYR* 6.5 0.2 - - + -
564C GLN* 3.0 34.7 + - + +
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Residues in contact with ARG 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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521A PHE* 4.3 10.7 - - + -
524A HIS* 5.5 1.6 + - - -
525A LEU* 5.3 0.7 - - - -
529A GLU* 3.1 60.4 + - - +
530A PRO* 4.2 15.7 + - - +
531A LEU* 4.0 21.0 - - + +
561A ARG* 3.2 45.0 + - - +
562A SER* 4.3 2.9 - - - +
563A TYR 3.1 1.4 + - - -
564A GLN* 1.3 79.4 - - + +
566A PHE* 1.3 58.7 + - - +
568A ALA* 3.4 5.0 + - - +
569A PHE* 3.0 25.1 + - - +
557C SER* 4.4 18.1 + - - -
560C GLU* 4.6 11.0 - - - +
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Residues in contact with PHE 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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517A LEU* 4.0 20.0 - - + -
518A ASN* 5.7 0.4 - - - -
521A PHE* 3.7 38.8 - + + -
535A PHE* 4.0 6.3 - - + -
537A ILE* 3.4 49.8 - - + -
539A VAL* 4.0 9.9 - - + -
562A SER 3.4 13.9 + - - +
563A TYR 3.1 3.3 + - - +
565A ARG* 1.3 75.2 - - - +
567A THR* 1.3 67.0 + - - +
568A ALA 3.1 1.3 - - - -
569A PHE* 3.6 22.0 - + - -
570A TYR* 2.9 27.6 + + + +
579A LEU* 3.7 20.0 - - + -
581A TRP* 4.1 8.3 - + + -
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Residues in contact with THR 567 (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 TYR* 2.8 47.0 + - + +
564A GLN* 3.9 6.1 - - - -
566A PHE* 1.3 80.7 - - - +
568A ALA* 1.3 61.1 + - - +
570A TYR* 3.8 5.8 - - + +
571A ALA* 3.2 21.8 + - - +
579A LEU* 5.4 9.9 - - + -
581A TRP* 4.1 10.0 - - - +
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Residues in contact with ALA 568 (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 GLN 3.2 14.5 + - - +
565A ARG* 3.7 4.7 - - - +
566A PHE 3.1 0.2 - - - -
567A THR* 1.3 78.8 - - - +
569A PHE* 1.3 65.5 + - - +
571A ALA* 3.3 16.2 + - - +
572A SER* 3.4 9.9 + - - -
555C LEU 6.0 1.8 - - - +
560C GLU* 4.0 12.1 - - - +
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Residues in contact with PHE 569 (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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517A LEU* 3.5 27.1 - - + -
520A GLN* 3.9 32.3 - - + -
521A PHE* 3.4 44.9 - + + -
524A HIS* 4.0 31.4 - + + +
565A ARG 3.0 17.5 + - - +
566A PHE* 3.7 15.7 - + - +
567A THR 3.3 0.4 - - - -
568A ALA* 1.3 78.4 - - - +
570A TYR* 1.3 60.6 + - - +
572A SER* 2.7 34.5 + - - -
573A ARG 4.3 0.5 + - - -
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Residues in contact with TYR 570 (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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517A LEU* 3.7 30.0 - - + +
539A VAL* 3.9 9.4 - - + +
566A PHE* 2.9 33.8 + + + +
567A THR* 3.8 4.9 - - + +
568A ALA 3.2 0.2 - - - -
569A PHE* 1.3 76.9 - + - +
571A ALA* 1.3 61.5 + - - +
572A SER 3.0 6.5 + - - -
573A ARG 3.7 1.4 + - - -
574A HIS* 3.2 50.6 + + - +
577A ARG* 3.5 39.1 + - + -
578A LYS 5.0 0.7 - - - -
579A LEU* 3.9 30.7 - - + -
33B TRP* 3.3 33.1 - - + +
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Residues in contact with ALA 571 (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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567A THR 3.2 13.4 + - - +
568A ALA* 3.3 12.9 + - - +
570A TYR* 1.3 78.4 - - - +
572A SER* 1.3 63.8 + - - +
574A HIS 3.2 19.3 - - - +
575A SER* 5.0 0.7 - - - -
577A ARG 6.2 0.2 - - - -
630C GLN* 5.9 0.2 + - - -
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Residues in contact with SER 572 (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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568A ALA 3.4 9.3 + - - -
569A PHE* 2.7 30.2 + - - -
570A TYR 3.0 1.4 - - - -
571A ALA* 1.3 82.0 - - - +
573A ARG* 1.3 62.5 + - - -
574A HIS 3.4 0.5 + - - -
630C GLN* 5.3 12.5 + - - +
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Residues in contact with ARG 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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569A PHE 4.3 0.6 + - - -
570A TYR 3.7 3.6 + - - -
571A ALA 3.6 0.2 - - - -
572A SER* 1.3 79.2 - - - +
574A HIS* 1.3 86.5 + - + +
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Residues in contact with HIS 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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517A LEU* 5.2 6.7 - - + +
570A TYR* 3.2 52.5 + + - +
571A ALA* 3.2 23.6 + - - +
572A SER 3.3 1.6 - - - -
573A ARG* 1.3 108.6 - - + +
575A SER* 1.3 61.8 + - - +
576A GLY 4.7 0.4 - - - +
577A ARG* 3.3 60.9 + - + +
35B TRP* 5.8 0.4 - - + -
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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