Contacts of the helix formed by residues 566 - 580 (chain H) 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 PRO 566 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567H LEU* 1.3 66.6 + - - +
568H THR* 3.2 6.0 + - - +
569H VAL* 3.6 28.2 + - + +
570H LEU* 3.9 5.9 + - - +
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Residues in contact with LEU 567 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H PRO* 1.3 77.7 - - - +
568H THR* 1.3 56.1 + - - +
570H LEU* 2.9 12.5 + - + +
571H LEU* 2.7 52.2 + - + +
621H TYR 5.3 5.6 - - - +
622H LYS 5.8 1.6 - - - +
623H ASN* 5.5 9.4 - - - -
624H LEU 5.8 0.9 - - - +
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Residues in contact with THR 568 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566H PRO* 3.2 3.0 - - - +
567H LEU* 1.3 77.9 + - - +
569H VAL* 1.3 65.8 + - - +
571H LEU* 4.0 1.2 - - - +
572H ARG* 3.0 50.4 + - - +
616H LEU* 4.0 35.1 - - + +
617H GLU* 5.3 2.0 - - - -
619H GLN* 5.7 6.5 - - - +
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Residues in contact with VAL 569 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H PRO* 3.7 22.9 - - + +
568H THR* 1.3 80.5 - - - +
570H LEU* 1.3 62.9 + - - +
572H ARG* 3.6 16.8 - - - +
573H SER* 3.3 19.3 + - - -
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Residues in contact with LEU 570 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H PRO 4.3 5.2 - - - +
567H LEU* 2.9 15.5 + - + +
569H VAL* 1.3 81.0 - - + +
571H LEU* 1.3 62.6 + - + +
573H SER* 3.0 15.7 + - - +
574H VAL* 2.8 37.8 + - + +
624H LEU* 5.0 3.8 - - + -
666H ALA* 4.2 22.0 - - + +
669H GLU* 4.7 16.8 - - + -
670H VAL* 4.2 25.6 - - + +
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Residues in contact with LEU 571 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H LEU* 2.7 37.2 + - + +
568H THR* 4.9 0.4 - - - +
570H LEU* 1.3 75.5 - - + +
572H ARG* 1.3 56.1 - - - +
574H VAL* 3.0 9.0 + - + +
575H LEU* 2.7 37.1 + - - +
616H LEU* 3.6 24.2 - - + -
621H TYR* 4.0 28.7 - - + +
623H ASN 4.8 6.3 - - - +
624H LEU* 4.7 20.6 - - + -
627H PHE* 3.6 41.5 - - + -
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Residues in contact with ARG 572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654F ARG* 5.6 11.4 - - - +
658F GLN* 4.8 23.1 + - - +
568H THR* 3.0 44.3 + - - +
569H VAL* 3.6 16.2 - - - +
571H LEU* 1.3 74.6 - - - +
573H SER* 1.3 58.4 + - - +
575H LEU* 3.7 2.0 - - - +
576H ASP* 3.1 46.6 + - - +
613H ARG* 4.4 5.8 + - - +
616H LEU* 3.7 14.9 - - + +
617H GLU* 3.1 32.6 + - - +
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Residues in contact with SER 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569H VAL* 3.3 8.9 + - - -
570H LEU* 3.0 24.1 + - - +
572H ARG* 1.3 78.8 - - - +
574H VAL* 1.3 62.9 + - - +
576H ASP* 3.4 10.6 + - - +
577H GLN* 3.0 34.4 + - - +
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Residues in contact with VAL 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H LEU* 2.8 29.8 + - + +
571H LEU* 3.4 14.4 - - + +
573H SER* 1.3 77.6 - - - +
575H LEU* 1.3 51.8 + - - +
577H GLN* 2.9 7.2 + - - +
578H LEU* 2.7 40.4 + - + +
627H PHE* 3.7 22.4 - - + -
662H VAL* 3.9 20.4 - - + +
663H LEU* 3.9 19.7 - - + -
666H ALA* 3.6 25.1 - - + -
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Residues in contact with LEU 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571H LEU 2.7 18.9 + - - +
572H ARG* 3.7 5.8 - - - +
574H VAL* 1.3 76.0 - - - +
576H ASP* 1.3 56.9 + - - +
578H LEU* 3.2 4.7 + - + +
579H GLN* 2.7 34.2 + - - +
609H PHE* 3.6 35.9 - - + +
612H MET* 4.3 11.7 - - + -
613H ARG* 3.4 59.0 - - + +
616H LEU* 4.0 12.3 - - + -
627H PHE* 3.9 19.7 - - + -
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Residues in contact with ASP 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654F ARG* 4.8 13.2 - - - -
572H ARG* 3.1 26.2 + - - +
573H SER* 3.7 9.1 - - - +
575H LEU* 1.3 75.1 - - - +
577H GLN* 1.3 58.9 + - + +
579H GLN* 3.4 2.8 + - - +
580H ASP* 3.0 38.6 + - - +
613H ARG* 2.8 39.7 + - - +
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Residues in contact with GLN 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573H SER* 3.0 22.2 + - - +
574H VAL* 2.9 9.9 + - - +
576H ASP* 1.3 77.1 - - + +
578H LEU* 1.3 61.9 + - - +
580H ASP* 3.4 18.1 + - - +
581H LYS* 3.4 26.3 + - - +
662H VAL* 3.6 31.4 - - + +
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Residues in contact with LEU 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574H VAL* 2.7 23.0 + - + +
575H LEU* 3.2 11.2 + - + +
577H GLN* 1.3 74.1 - - - +
579H GLN* 1.3 59.5 + - - +
581H LYS* 2.9 27.5 + - + +
582H ASP 3.6 3.1 + - - -
609H PHE* 4.0 18.1 - - + -
612H MET* 5.1 0.2 - - + -
627H PHE* 3.7 33.2 - - + -
631H PHE* 4.0 28.3 - - + -
655H LEU* 4.1 7.3 - - + +
659H GLY* 3.5 38.1 - - - +
662H VAL* 4.1 11.2 - - + -
663H LEU* 4.8 4.7 - - + -
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Residues in contact with GLN 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575H LEU* 2.7 21.2 + - - +
576H ASP* 3.8 5.2 - - - +
578H LEU* 1.3 73.7 - - - +
580H ASP* 1.3 57.0 + - - +
582H ASP* 3.1 27.8 + - - +
583H PRO* 4.8 0.5 - - - +
585H ARG* 5.7 7.5 - - - +
588H ALA* 3.8 22.0 + - - +
609H PHE* 3.2 48.3 - - + +
610H ALA* 4.8 0.6 - - - +
613H ARG* 2.7 41.1 + - - +
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Residues in contact with ASP 580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576H ASP* 3.0 28.0 + - - +
577H GLN* 3.5 16.1 - - - +
578H LEU 3.1 0.4 - - - -
579H GLN* 1.3 73.0 - - - +
581H LYS* 1.3 65.3 + - + +
582H ASP 3.1 5.6 + - - -
583H PRO* 3.8 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