Contacts of the helix formed by residues 608 - 617 (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 ASP 608 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587H PHE* 3.5 14.4 - - - +
588H ALA 3.5 1.2 - - - +
589H GLN 3.6 13.0 - - - +
590H PRO* 3.1 33.1 - - + +
606H PRO 5.4 0.5 - - - -
607H MET* 1.3 81.6 - - - +
609H PHE* 1.3 65.2 + - - +
610H ALA* 3.0 31.7 + - - +
611H THR* 2.5 31.8 + - - -
612H MET* 3.0 21.5 + - - +
634H ILE* 3.7 15.3 - - - -
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Residues in contact with PHE 609 (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* 3.6 20.3 - - + +
578H LEU* 4.0 29.8 - - + -
579H GLN* 3.2 48.2 - - + +
582H ASP* 4.1 15.5 - - + -
587H PHE* 3.1 33.8 + - + +
588H ALA 4.1 0.2 - - - +
608H ASP* 1.3 74.2 - - - +
610H ALA* 1.3 57.4 + - - +
612H MET* 3.1 8.6 + - - +
613H ARG* 2.8 33.9 + - - +
631H PHE* 4.2 11.2 - + - -
634H ILE* 3.6 19.9 - - + +
655H LEU* 3.9 20.4 - - + -
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Residues in contact with ALA 610 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579H GLN* 4.8 1.3 - - - +
588H ALA 3.1 16.5 + - - +
589H GLN* 3.6 28.7 - - - +
590H PRO* 4.7 1.3 - - + -
608H ASP* 3.0 10.9 + - - +
609H PHE* 1.3 74.3 - - - +
611H THR* 1.3 62.7 + - - +
613H ARG* 3.2 12.7 + - - +
614H LYS* 3.1 24.9 + - - +
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Residues in contact with THR 611 (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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590H PRO* 4.0 8.1 - - - +
606H PRO 5.7 1.6 - - - +
607H MET* 3.8 25.6 - - + +
608H ASP* 2.5 35.7 + - - -
610H ALA* 1.3 77.4 - - - +
612H MET* 1.3 62.2 + - - +
614H LYS* 3.5 8.5 + - + +
615H ARG* 3.2 22.6 + - + +
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Residues in contact with MET 612 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575H LEU* 4.3 9.4 - - + -
578H LEU* 5.1 0.9 - - + -
607H MET* 3.9 6.3 - - - -
608H ASP 3.0 14.2 + - - +
609H PHE* 3.5 18.6 - - - +
611H THR* 1.3 73.9 - - - +
613H ARG* 1.3 53.9 + - - +
615H ARG 3.3 1.0 + - - -
616H LEU* 2.8 37.3 + - - +
621H TYR* 3.3 22.2 - - + +
627H PHE* 3.5 58.1 - - + +
630H ASP* 3.8 12.1 - - + -
631H PHE* 3.8 17.0 - - + +
634H ILE* 3.6 28.7 - - - -
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Residues in contact with ARG 613 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572H ARG* 4.4 11.5 + - - +
575H LEU* 3.4 28.1 - - + +
576H ASP* 2.8 32.5 + - - +
579H GLN* 2.7 36.5 + - - +
609H PHE 2.8 24.2 + - - +
610H ALA* 3.2 12.6 - - - +
612H MET* 1.3 70.3 - - - +
614H LYS* 1.3 59.2 + - + +
616H LEU* 3.2 6.2 + - - +
617H GLU* 2.8 51.5 + - + +
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Residues in contact with LYS 614 (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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610H ALA 3.1 11.1 + - - +
611H THR* 3.7 12.8 - - + +
612H MET 3.2 0.4 - - - -
613H ARG* 1.3 78.8 - - + +
615H ARG* 1.3 64.3 + - - +
617H GLU* 3.0 14.6 + - - -
618H ALA* 3.1 14.7 + - - +
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Residues in contact with ARG 615 (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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607H MET* 5.9 1.1 - - - +
611H THR* 3.2 15.2 + - + +
614H LYS* 1.3 79.8 - - - +
616H LEU* 1.3 58.2 + - - +
618H ALA* 3.4 6.8 + - - +
620H GLY* 2.7 56.0 + - - -
621H TYR* 3.2 30.0 - - + +
622H LYS* 5.6 0.2 - - - +
626H GLU* 2.8 44.4 + - - +
629H GLU* 6.1 0.4 - - - +
630H ASP* 3.3 26.6 + - - -
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Residues in contact with LEU 616 (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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568H THR* 4.0 27.9 - - + +
571H LEU* 3.6 36.1 - - + -
572H ARG* 3.7 31.2 - - + +
575H LEU* 4.0 22.9 - - + -
612H MET 2.8 20.3 + - - +
613H ARG* 3.2 5.4 - - - +
615H ARG* 1.3 73.9 - - - +
617H GLU* 1.3 69.8 + - + +
618H ALA 3.2 0.2 - - - -
619H GLN* 3.1 19.2 + - - -
620H GLY 4.8 0.2 - - - +
621H TYR* 3.5 16.9 + - + +
627H PHE* 4.6 3.1 - - + -
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Residues in contact with GLU 617 (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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657F ASP* 5.4 6.4 - - - +
568H THR* 5.3 3.4 - - - -
572H ARG* 3.1 39.9 + - - +
613H ARG* 2.8 39.7 + - - +
614H LYS* 3.0 4.7 + - - +
616H LEU* 1.3 85.1 - - + +
618H ALA* 1.3 57.6 + - - +
619H GLN 3.5 0.9 - - - -
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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