Contacts of the helix formed by residues 615 - 624 (chain R) in PDB entry 1HI0
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 615 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613R GLU 4.7 3.6 - - - +
614R LEU* 1.3 76.2 - - - +
616R PRO* 1.3 77.5 - - - +
617R ILE* 2.9 21.8 + - - +
618R ASP* 2.7 37.0 + - - +
619R LEU* 3.0 15.1 + - - +
636R ASP 5.1 2.1 + - - +
638R SER* 3.5 10.1 - - - +
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Residues in contact with PRO 616 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553R SER* 3.7 15.9 - - - -
556R ASP* 3.5 42.4 - - + +
557R THR* 5.4 2.7 - - - +
614R LEU 4.9 0.4 - - - +
615R THR* 1.3 90.7 - - - +
617R ILE* 1.3 65.0 + - + +
619R LEU* 3.1 8.1 + - + +
620R GLU* 3.0 28.6 + - - +
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Residues in contact with ILE 617 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305R THR* 5.1 10.5 - - - +
306R THR* 5.5 7.4 - - + -
615R THR* 2.9 9.9 + - - +
616R PRO* 1.3 82.1 - - + +
618R ASP* 1.3 64.5 + - - +
620R GLU* 3.1 1.9 + - - +
621R VAL* 2.9 21.9 + - + +
632R TRP* 3.8 58.3 - - + +
636R ASP* 3.4 32.3 - - + +
637R VAL* 3.9 15.7 - - + -
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Residues in contact with ASP 618 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614R LEU* 3.6 19.7 - - + +
615R THR* 2.7 35.6 + - - +
617R ILE* 1.3 78.8 - - - +
619R LEU* 1.3 56.5 + - - +
621R VAL* 3.4 5.6 + - - +
622R LEU* 3.0 34.3 + - - +
636R ASP 4.7 0.3 - - - +
637R VAL* 3.7 11.0 - - - +
638R SER* 2.5 50.4 + - - -
641R ILE* 4.3 11.7 - - + +
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Residues in contact with LEU 619 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549R LEU* 4.1 26.4 - - + +
552R ALA* 3.3 32.5 - - + +
553R SER* 3.8 20.9 - - - +
611R LEU* 4.1 20.4 - - + -
614R LEU* 3.8 33.7 - - + +
615R THR 3.0 13.2 + - - +
616R PRO* 3.1 8.5 + - + +
618R ASP* 1.3 75.3 - - - +
620R GLU* 1.3 66.9 + - - +
622R LEU* 3.1 14.8 + - + +
623R ALA* 3.1 15.3 + - - +
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Residues in contact with GLU 620 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524R ASN* 5.1 3.3 - - - +
550R ALA* 4.1 14.5 - - - +
553R SER* 2.6 27.3 + - - +
554R MET* 4.3 0.9 + - - -
557R THR* 3.2 33.2 + - - +
558R TYR* 4.7 7.3 + - - -
616R PRO 3.0 18.1 + - - +
617R ILE 3.7 2.9 - - - +
619R LEU* 1.3 74.6 - - - +
621R VAL* 1.3 57.0 + - - +
623R ALA* 3.4 6.1 + - - +
624R ASP* 2.9 31.0 + - - +
627R LYS* 3.9 22.2 + - + +
632R TRP* 3.8 25.1 - - + -
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Residues in contact with VAL 621 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617R ILE* 2.9 20.7 + - + +
618R ASP* 3.7 5.6 - - - +
620R GLU* 1.3 74.3 - - - +
622R LEU* 1.3 62.5 + - + +
624R ASP 3.9 5.6 - - - -
625R PRO* 2.9 34.4 - - + +
627R LYS* 5.1 0.4 - - + -
628R LEU* 4.1 27.8 - - + +
632R TRP* 3.8 23.8 - - + -
637R VAL* 4.0 25.1 - - + -
641R ILE* 5.5 2.0 - - + -
645R LEU* 3.5 24.0 - - + +
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Residues in contact with LEU 622 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545R PRO* 3.2 15.8 - - - +
546R PHE* 3.1 42.1 + - + -
549R LEU* 3.6 27.6 - - + -
598R LEU* 3.8 21.8 - - + -
614R LEU* 4.2 12.3 - - + -
618R ASP 3.0 22.4 + - - +
619R LEU* 3.1 5.6 + - - +
621R VAL* 1.3 77.4 - - - +
623R ALA* 1.3 56.7 + - - +
641R ILE* 3.8 27.8 - - + -
644R VAL* 4.7 7.2 - - + -
645R LEU* 4.6 19.3 - - + -
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Residues in contact with ALA 623 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544R ARG* 3.5 30.7 + - - +
546R PHE 3.6 23.1 + - - +
547R PRO* 4.3 6.2 - - + +
550R ALA* 4.0 26.0 - - + +
619R LEU 3.1 14.3 + - - +
620R GLU* 3.9 4.5 - - - +
622R LEU* 1.3 77.8 - - - +
624R ASP* 1.3 63.0 + - + +
625R PRO* 3.9 1.6 - - - -
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Residues in contact with ASP 624 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530R TYR* 5.9 1.6 - - - -
543R LYS 4.3 5.7 - - - +
544R ARG* 5.4 3.0 - - + +
620R GLU 2.9 12.9 + - - +
621R VAL* 3.1 5.8 - - - +
623R ALA* 1.3 82.1 - - + +
625R PRO* 1.3 60.9 - - - +
626R ASN* 2.8 36.8 + - - +
627R LYS* 3.0 52.6 + - - +
630R TYR* 4.2 3.8 + - - -
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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