Contacts of the helix formed by residues 610 - 622 (chain A) in PDB entry 3PE3
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 CYS 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A LEU* 4.2 16.2 - - - -
608A ILE* 3.2 3.6 - - + +
609A PRO* 1.3 80.8 - - + +
611A ASN* 1.3 65.2 + - - +
612A GLY* 3.1 17.7 + - - -
613A LYS* 3.1 31.5 + - + +
614A ALA* 2.9 23.4 + - - +
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Residues in contact with ASN 611 (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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524A LYS* 5.5 5.7 + - - +
525A ILE* 5.4 0.4 - - - +
528A LEU* 4.7 7.6 - - + +
609A PRO 3.3 5.6 + - - +
610A CYS* 1.3 72.0 - - - +
612A GLY* 1.3 56.9 + - - +
614A ALA 3.8 0.2 - - - -
615A ALA* 2.9 32.1 + - - +
637A ARG* 3.1 35.8 + - - +
639A GLU* 3.2 47.1 + - + +
640A LEU* 3.7 10.3 - - + +
643A LEU* 3.6 9.8 - - + +
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Residues in contact with GLY 612 (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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528A LEU* 3.8 20.5 - - - +
530A LYS* 3.5 26.4 + - - -
610A CYS* 3.1 11.9 - - - -
611A ASN* 1.3 79.7 - - - +
613A LYS* 1.3 62.1 + - - +
615A ALA* 3.9 0.7 - - - +
616A ASP* 3.1 26.0 + - - -
643A LEU* 4.3 0.9 - - - -
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Residues in contact with LYS 613 (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 LYS* 5.9 0.4 - - - +
608A ILE* 3.7 20.6 - - + +
610A CYS* 3.1 24.2 + - + +
612A GLY* 1.3 74.9 - - - +
614A ALA* 1.3 60.5 + - - +
616A ASP* 3.5 12.7 - - - +
617A ARG* 3.2 20.4 + - - +
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Residues in contact with ALA 614 (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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605A LEU* 4.3 16.2 - - + +
608A ILE* 3.7 13.4 - - + +
610A CYS 2.9 16.9 + - - +
613A LYS* 1.3 75.6 - - - +
615A ALA* 1.3 65.9 + - - +
617A ARG* 3.1 16.0 + - - +
618A ILE* 3.1 17.2 + - - +
637A ARG* 3.5 14.8 - - - +
640A LEU* 3.5 22.2 - - + -
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Residues in contact with ALA 615 (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 TYR* 3.6 17.3 - - + +
611A ASN 2.9 18.7 + - - +
612A GLY 3.9 0.4 - - - +
614A ALA* 1.3 73.5 - - - +
616A ASP* 1.3 66.5 + - - +
618A ILE* 3.2 11.3 + - - +
619A HIS* 2.9 23.4 + - - +
640A LEU* 3.8 10.4 - - + +
643A LEU* 3.7 26.0 - - + -
645A PRO* 3.6 11.3 - - + +
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Residues in contact with ASP 616 (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 LYS* 3.0 24.8 + - - -
533A TYR* 2.6 34.0 + - - -
612A GLY 3.1 14.8 + - - +
613A LYS* 3.5 16.4 - - - +
614A ALA 3.2 0.2 - - - -
615A ALA* 1.3 77.2 - - - +
617A ARG* 1.3 56.9 + - - +
619A HIS* 3.2 2.1 + - - +
620A GLN* 2.8 51.4 + - - +
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Residues in contact with ARG 617 (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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581A TYR* 4.7 1.1 - - + -
601A HIS* 6.0 0.4 + - - +
603A ILE* 3.2 49.7 - - + +
605A LEU* 4.4 8.1 - - + -
608A ILE* 4.5 12.2 - - + +
613A LYS 3.2 9.8 + - - +
614A ALA* 3.1 13.3 + - - +
616A ASP* 1.3 78.4 - - - +
618A ILE* 1.3 63.6 + - - +
620A GLN* 3.2 18.2 + - - +
621A ASP* 3.1 50.0 + - - +
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Residues in contact with ILE 618 (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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551A VAL* 4.7 5.6 - - + -
581A TYR* 3.7 28.3 - - + -
605A LEU* 4.3 15.5 - - + -
614A ALA 3.1 12.0 + - - +
615A ALA* 3.2 11.0 + - - +
617A ARG* 1.3 76.9 - - - +
619A HIS* 1.3 64.7 + - - +
621A ASP* 3.2 13.9 + - - +
622A GLY 3.4 7.1 + - - -
623A ILE* 3.5 25.8 + - + +
626A LEU* 3.8 31.6 - - + -
640A LEU* 4.6 14.8 - - + -
645A PRO* 3.8 24.5 - - + -
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Residues in contact with HIS 619 (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 TYR* 3.3 44.1 - + + +
534A GLU* 2.9 31.5 + - + -
535A HIS* 4.8 2.2 - + - -
536A PRO* 5.7 3.1 - - + +
615A ALA 2.9 15.7 + - - +
616A ASP* 3.6 4.8 + - - +
618A ILE* 1.3 76.0 - - - +
620A GLN* 1.3 64.6 + - - +
622A GLY* 3.0 20.3 + - - +
623A ILE 5.2 0.9 - - - +
645A PRO* 3.6 27.1 - - + -
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Residues in contact with GLN 620 (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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616A ASP* 2.8 35.8 + - + +
617A ARG* 3.2 20.5 + - - +
619A HIS* 1.3 83.3 - - - +
621A ASP* 1.3 63.8 + - - +
622A GLY* 3.4 0.9 + - - -
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Residues in contact with ASP 621 (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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547A ARG* 3.5 25.8 + - - -
579A PHE* 3.8 27.4 - - + -
581A TYR* 2.7 36.6 + - - +
603A ILE* 4.0 0.9 - - - +
617A ARG* 3.1 47.0 + - - +
618A ILE 3.2 4.2 + - - +
620A GLN* 1.3 77.4 - - - +
622A GLY* 1.3 61.3 + - - +
623A ILE* 3.5 2.2 - - + -
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Residues in contact with GLY 622 (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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536A PRO* 4.1 14.7 - - - +
547A ARG* 3.3 25.1 + - - +
618A ILE 3.4 0.8 + - - -
619A HIS 3.0 16.9 + - - -
620A GLN 3.1 1.7 - - - -
621A ASP* 1.3 80.5 - - - +
623A ILE* 1.3 66.7 + - - +
624A HIS* 3.4 9.4 + - - -
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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