Contacts of the helix formed by residues 565 - 580 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564F LEU* 1.3 73.5 - - - +
566F PRO* 1.3 75.0 - - - +
567F LEU* 3.7 7.6 + - - +
568F THR* 3.2 14.4 + - - -
569F VAL* 3.2 24.8 + - - +
619F GLN* 3.2 29.5 + - + +
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Residues in contact with PRO 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564F LEU 4.6 0.7 - - - +
565F THR* 1.3 87.4 - - - +
567F LEU* 1.3 66.4 + - - +
569F VAL* 3.0 10.2 + - + +
570F LEU* 3.0 27.9 + - - +
673F ILE* 5.2 17.0 - - + -
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Residues in contact with LEU 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F THR* 3.4 8.1 + - - +
566F PRO* 1.3 79.7 - - - +
568F THR* 1.3 56.9 + - - +
570F LEU* 3.4 10.2 + - + +
571F LEU* 2.9 59.6 + - + +
621F TYR 3.8 11.9 - - - +
622F LYS* 3.4 15.7 - - - +
623F ASN* 3.4 32.3 - - - +
624F LEU* 4.3 12.6 - - + +
670F VAL* 4.9 13.5 - - + -
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Residues in contact with THR 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564F LEU* 4.6 17.3 - - + -
565F THR* 3.2 12.6 + - - +
566F PRO 3.1 1.0 - - - -
567F LEU* 1.3 77.8 - - - +
569F VAL* 1.3 58.3 + - - +
571F LEU* 3.3 3.3 + - - +
572F ARG* 2.8 32.4 + - + +
616F LEU* 3.9 33.9 - - + +
617F GLU* 5.9 0.2 - - - -
619F GLN* 2.8 43.0 + - + +
621F TYR* 5.1 5.9 + - - +
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Residues in contact with VAL 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564F LEU* 3.9 31.0 - - + +
565F THR 3.2 15.9 - - - +
566F PRO* 3.0 9.1 + - + +
568F THR* 1.3 77.4 - - + +
570F LEU* 1.3 64.1 + - + +
572F ARG* 3.2 9.6 + - - +
573F SER* 3.1 21.4 + - - -
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Residues in contact with LEU 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F EDO 3.4 31.2 + - - +
566F PRO 3.0 15.2 + - - +
567F LEU* 3.7 14.1 - - + +
569F VAL* 1.3 77.8 - - + +
571F LEU* 1.3 58.6 + - + +
573F SER* 3.2 6.4 + - - -
574F VAL* 2.8 33.5 + - + +
666F ALA* 5.3 4.0 - - + +
669F GLU* 3.8 26.0 - - + -
670F VAL* 4.7 16.8 - - + -
673F ILE* 3.5 30.5 - - + -
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Residues in contact with LEU 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567F LEU* 2.9 52.5 + - + +
568F THR* 5.0 0.7 - - - +
570F LEU* 1.3 74.8 - - + +
572F ARG* 1.3 52.8 + - - +
574F VAL* 3.5 8.8 - - + +
575F LEU* 2.6 36.4 + - - +
616F LEU* 3.6 20.9 - - + -
621F TYR* 3.4 33.9 - - + -
623F ASN 4.9 0.9 - - - +
624F LEU* 3.9 27.8 - - + -
627F PHE* 3.7 30.8 - - + -
666F ALA* 6.0 0.4 - - + -
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Residues in contact with ARG 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564F LEU* 6.4 1.8 - - - -
568F THR* 2.8 20.9 + - + +
569F VAL* 3.2 11.4 + - - +
571F LEU* 1.3 72.1 - - - +
573F SER* 1.3 57.1 + - - +
575F LEU* 3.1 2.6 + - - +
576F ASP* 2.9 48.5 + - - +
613F ARG* 3.5 25.3 - - - +
616F LEU* 3.4 19.1 - - + +
617F GLU* 3.1 37.2 + - - +
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Residues in contact with SER 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F EDO 2.6 40.1 + - - -
569F VAL* 3.1 12.2 + - - -
570F LEU* 3.4 9.9 - - - -
572F ARG* 1.3 71.0 - - - +
574F VAL* 1.3 68.2 + - - +
576F ASP* 3.3 6.7 + - - +
577F GLN* 3.0 32.7 + - - +
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Residues in contact with VAL 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F EDO 4.1 11.9 - - - +
570F LEU* 2.8 25.0 + - + +
571F LEU* 3.5 13.2 - - + +
573F SER* 1.3 73.6 - - - +
575F LEU* 1.3 63.2 + - - +
577F GLN* 3.2 1.9 + - - +
578F LEU* 2.9 44.6 + - + +
627F PHE* 3.6 12.8 - - + -
662F VAL* 3.9 22.0 - - + -
663F LEU* 4.1 11.7 - - + -
666F ALA* 3.6 28.7 - - + -
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Residues in contact with LEU 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571F LEU 2.6 20.6 + - - +
572F ARG* 3.1 4.7 + - - +
574F VAL* 1.3 72.4 - - - +
576F ASP* 1.3 59.0 + - - +
578F LEU* 3.1 10.7 + - + +
579F GLN* 2.9 33.1 + - + +
609F PHE* 3.4 44.0 - - + +
612F MET* 4.2 14.1 - - + +
613F ARG* 3.7 53.8 - - + +
616F LEU* 4.0 16.2 - - + -
627F PHE* 3.9 14.6 - - + -
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Residues in contact with ASP 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572F ARG* 2.9 38.2 + - - +
573F SER* 3.9 6.2 + - - +
575F LEU* 1.3 75.6 - - - +
577F GLN* 1.3 58.8 + - + +
579F GLN* 3.1 6.2 + - - +
580F ASP* 2.9 36.9 + - - +
613F ARG* 2.8 39.9 + - - +
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Residues in contact with GLN 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F EDO 3.4 22.0 + - - -
573F SER* 3.0 37.4 + - - +
574F VAL 3.5 4.2 - - - +
576F ASP* 1.3 77.3 - - + +
578F LEU* 1.3 63.1 - - - +
580F ASP* 3.4 17.5 + - - +
581F LYS* 3.3 28.8 + - - +
662F VAL* 3.8 31.7 - - + +
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Residues in contact with LEU 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F VAL* 2.9 37.7 + - + +
575F LEU* 3.4 7.9 - - + +
577F GLN* 1.3 77.6 - - - +
579F GLN* 1.3 60.1 + - - +
581F LYS* 3.2 20.3 + - - +
582F ASP 3.8 0.5 + - - -
609F PHE* 3.8 18.7 - - + -
612F MET* 5.4 0.4 - - + -
627F PHE* 3.7 20.0 - - + -
631F PHE* 4.1 29.4 - - + -
655F LEU* 3.6 13.0 - - + +
659F GLY* 4.3 15.5 - - - +
662F VAL* 3.7 32.1 - - + -
663F LEU* 4.9 4.5 - - + -
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Residues in contact with GLN 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F LEU* 2.9 19.6 + - + +
576F ASP* 3.1 8.3 + - - +
578F LEU* 1.3 69.7 - - - +
580F ASP* 1.3 59.0 + - - +
581F LYS 3.0 4.9 - - - -
582F ASP* 2.9 29.6 + - - +
583F PRO* 4.8 1.0 - - - +
585F ARG* 5.1 6.3 - - - +
588F ALA* 4.3 16.2 + - - +
609F PHE* 3.6 51.3 - - + +
610F ALA* 5.2 0.3 + - - -
613F ARG* 2.7 34.4 + - - +
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Residues in contact with ASP 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576F ASP* 2.9 19.9 + - - +
577F GLN* 3.4 18.7 - - - +
578F LEU 3.2 0.2 - - - -
579F GLN* 1.3 78.3 - - - +
581F LYS* 1.3 65.0 + - + +
582F ASP 3.3 1.5 + - - -
583F PRO* 4.4 12.9 - - - +
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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