Contacts of the helix formed by residues 565 - 581 (chain A) in PDB entry 3RCW
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 565 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ARG 4.7 2.2 - - - +
564A LEU* 1.3 76.0 - - - +
566A PRO* 1.3 76.0 - - - +
567A LEU* 3.3 9.8 + - - +
568A THR* 3.3 21.5 + - - -
569A VAL* 3.2 19.9 + - - +
619A GLN* 3.2 21.3 + - + +
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Residues in contact with PRO 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU 4.4 2.0 - - - +
565A THR* 1.3 90.2 - - - +
567A LEU* 1.3 63.2 + - - +
569A VAL* 3.3 9.7 + - + +
570A LEU* 3.0 23.4 + - - +
673A ILE* 5.0 27.0 - - + +
677A GLU* 6.2 0.2 - - - +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A THR* 3.2 9.6 + - - +
566A PRO* 1.3 79.0 - - - +
568A THR* 1.3 52.5 + - - +
570A LEU* 3.1 9.1 + - + +
571A LEU* 2.8 64.0 + - + +
621A TYR 3.9 11.0 - - - +
622A LYS 3.5 15.7 - - - +
623A ASN* 3.5 31.0 - - - +
624A LEU 4.3 9.0 - - - +
670A VAL* 4.5 22.9 - - + -
673A ILE* 6.3 0.2 - - - -
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Residues in contact with THR 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU* 4.2 21.5 - - + -
565A THR* 3.3 10.5 + - - -
567A LEU* 1.3 78.1 - - - +
569A VAL* 1.3 52.4 + - - +
571A LEU* 3.0 2.3 + - - +
572A ARG* 2.7 37.0 + - + +
616A LEU* 3.5 40.4 - - + +
617A GLU* 5.5 1.1 - - - -
619A GLN* 2.5 38.6 + - - +
621A TYR 5.2 4.2 + - - -
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Residues in contact with VAL 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU* 4.1 27.8 - - + +
565A THR 3.2 17.4 + - - +
566A PRO* 3.7 9.0 - - + +
568A THR* 1.3 74.9 - - - +
570A LEU* 1.3 64.7 + - - +
572A ARG* 3.4 7.3 + - - +
573A SER* 3.2 21.1 + - - -
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Residues in contact with LEU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PRO 3.0 13.1 + - - +
567A LEU* 3.4 13.5 - - + +
569A VAL* 1.3 79.3 - - - +
571A LEU* 1.3 59.7 + - + +
573A SER* 3.1 11.5 + - - -
574A VAL* 2.9 39.7 + - + +
666A ALA* 4.0 15.9 - - + +
669A GLU* 3.8 30.5 - - + -
670A VAL* 3.7 30.5 - - + +
673A ILE* 4.4 12.6 - - + -
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 2.8 48.8 + - + +
568A THR* 3.8 4.0 - - - +
570A LEU* 1.3 76.7 - - + +
572A ARG* 1.3 57.7 + - - +
574A VAL* 3.1 9.1 + - + +
575A LEU* 2.7 31.0 + - - +
616A LEU* 3.7 14.8 - - + -
621A TYR* 3.6 31.9 - - + -
623A ASN 4.5 2.5 - - - +
624A LEU* 3.8 29.4 - - + -
627A PHE* 4.0 29.0 - - + -
666A ALA* 5.9 0.4 - - + -
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Residues in contact with ARG 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU* 5.9 6.7 - - - -
568A THR* 2.7 23.1 + - + +
569A VAL* 3.7 6.7 - - - +
571A LEU* 1.3 72.4 - - - +
573A SER* 1.3 57.0 + - - +
575A LEU* 3.8 2.0 - - - +
576A ASP* 2.9 43.9 + - - +
613A ARG* 3.6 23.6 - - - +
616A LEU* 3.2 19.1 - - + +
617A GLU* 2.9 37.0 + - - +
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Residues in contact with SER 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A VAL* 3.2 10.0 + - - -
570A LEU* 3.1 16.6 + - - -
572A ARG* 1.3 76.8 - - - +
574A VAL* 1.3 69.6 + - - +
576A ASP* 4.0 6.1 - - - +
577A GLN* 3.2 37.8 + - - +
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 2.9 23.3 + - + +
571A LEU* 3.4 14.4 - - + +
573A SER* 1.3 75.7 - - - +
575A LEU* 1.3 57.9 + - - +
577A GLN* 2.9 14.9 + - - +
578A LEU* 2.9 34.3 + - + +
627A PHE* 3.6 24.0 - - + -
662A VAL* 4.5 12.1 - - + +
663A LEU* 3.7 20.0 - - + -
666A ALA* 3.6 28.9 - - + -
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU 2.7 19.4 + - - +
572A ARG* 3.8 5.8 - - - +
574A VAL* 1.3 74.0 - - - +
576A ASP* 1.3 56.6 + - - +
578A LEU* 3.3 4.1 + - + +
579A GLN* 3.0 26.4 + - + +
609A PHE* 3.5 36.8 - - + +
612A MET* 4.3 11.4 - - + -
613A ARG* 3.5 59.0 - - + +
616A LEU* 4.4 11.0 - - + -
627A PHE* 3.8 22.9 - - + -
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Residues in contact with ASP 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ARG* 2.9 36.7 + - - +
573A SER* 4.0 6.1 - - - +
575A LEU* 1.3 75.3 - - - +
577A GLN* 1.3 58.4 + - + +
579A GLN* 3.5 4.2 + - - +
580A ASP* 3.0 37.6 + - - +
613A ARG* 2.8 37.3 + - - +
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Residues in contact with GLN 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A SER* 3.2 35.8 + - - +
574A VAL* 2.9 10.2 + - - +
576A ASP* 1.3 74.1 - - + +
578A LEU* 1.3 67.2 + - - +
580A ASP* 3.2 17.1 + - - +
581A LYS* 3.1 35.1 + - - +
662A VAL* 3.9 32.0 - - + +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 2.9 22.1 + - + +
575A LEU* 3.6 7.2 - - + +
576A ASP 3.3 0.4 - - - -
577A GLN* 1.3 75.8 - - - +
579A GLN* 1.3 63.6 + - - +
581A LYS* 3.1 21.6 + - + +
582A ASP 3.6 1.0 + - - -
609A PHE* 3.8 19.2 - - + -
612A MET* 5.7 0.4 - - + -
627A PHE* 4.0 27.1 - - + -
631A PHE* 3.6 38.4 - - + -
655A LEU* 3.5 13.6 - - + +
659A GLY* 3.6 35.2 - - - +
662A VAL* 4.4 12.8 - - + -
663A LEU* 4.8 2.9 - - + -
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Residues in contact with GLN 579 (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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575A LEU* 3.0 18.9 + - + +
576A ASP* 3.8 6.3 - - - +
577A GLN 3.3 0.2 - - - -
578A LEU* 1.3 76.2 - - - +
580A ASP* 1.3 60.1 + - - +
582A ASP* 2.9 28.0 + - + +
583A PRO* 5.0 0.3 - - - +
585A ARG* 4.8 8.3 - - - +
588A ALA* 4.2 19.0 + - - +
609A PHE* 3.5 51.3 - - + +
610A ALA* 5.7 0.2 - - - -
613A ARG* 2.7 33.8 + - - +
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Residues in contact with ASP 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ASP* 3.0 27.1 + - - +
577A GLN* 3.5 18.4 - - - +
578A LEU 3.2 0.8 - - - -
579A GLN* 1.3 76.8 - - - +
581A LYS* 1.3 72.0 + - - +
582A ASP 3.2 1.5 + - - -
583A PRO* 3.9 12.1 - - - +
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Residues in contact with LYS 581 (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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577A GLN* 3.1 38.5 + - - +
578A LEU* 3.4 10.5 - - + +
579A GLN 3.1 0.8 - - - -
580A ASP* 1.3 89.0 + - - +
582A ASP* 1.3 55.0 + - - +
583A PRO* 3.1 14.7 - - - +
654A ARG* 6.2 0.2 - - - +
655A LEU* 3.5 21.5 - - + +
658A GLN* 3.6 44.4 - - + +
659A GLY 5.4 0.4 - - - +
662A VAL* 4.7 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
------------------------------------------------------------
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