Contacts of the helix formed by residues 615 - 624 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613Q GLU 4.7 3.8 - - - +
614Q LEU* 1.3 76.5 - - - +
616Q PRO* 1.3 76.8 - - - +
617Q ILE* 2.9 21.5 + - - +
618Q ASP* 2.7 37.4 + - - +
619Q LEU* 3.0 14.9 + - - +
636Q ASP 5.1 2.0 + - - +
638Q SER* 3.5 10.1 - - - +
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Residues in contact with PRO 616 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553Q SER* 3.7 14.8 - - - -
556Q ASP* 3.5 42.6 - - + +
557Q THR* 5.4 2.7 - - - +
614Q LEU 4.9 0.2 - - - +
615Q THR* 1.3 91.2 - - - +
617Q ILE* 1.3 65.4 + - + +
619Q LEU* 3.1 8.0 + - + +
620Q GLU* 3.0 28.7 + - - +
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Residues in contact with ILE 617 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q THR* 5.1 10.5 - - + +
306Q THR* 5.5 6.7 - - + -
615Q THR* 2.9 9.4 + - - +
616Q PRO* 1.3 82.9 - - + +
618Q ASP* 1.3 64.6 + - - +
620Q GLU* 3.1 1.4 + - - +
621Q VAL* 2.9 22.4 + - + +
632Q TRP* 3.8 57.4 - - + +
636Q ASP* 3.4 32.8 - - + +
637Q VAL* 3.9 16.2 - - + -
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Residues in contact with ASP 618 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614Q LEU* 3.6 19.1 - - + +
615Q THR* 2.7 35.7 + - - +
617Q ILE* 1.3 78.5 - - - +
619Q LEU* 1.3 57.3 + - - +
621Q VAL* 3.4 6.5 + - - +
622Q LEU* 3.0 34.9 + - - +
636Q ASP 4.7 0.5 - - - +
637Q VAL* 3.7 11.8 - - - +
638Q SER* 2.5 49.5 + - - -
641Q ILE* 4.3 12.6 - - + +
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Residues in contact with LEU 619 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549Q LEU* 4.1 26.2 - - + +
552Q ALA* 3.3 33.2 - - + +
553Q SER* 3.8 19.7 - - - +
611Q LEU* 4.1 19.7 - - + -
614Q LEU* 3.8 34.1 - - + +
615Q THR 3.0 13.2 + - - +
616Q PRO* 3.1 8.3 + - + +
618Q ASP* 1.3 73.4 - - - +
620Q GLU* 1.3 65.8 + - - +
622Q LEU* 3.1 15.0 + - - +
623Q ALA* 3.1 14.7 + - - +
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Residues in contact with GLU 620 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524Q ASN* 5.1 2.4 - - - +
550Q ALA* 4.1 14.5 - - - +
553Q SER* 2.6 28.0 + - - +
554Q MET* 4.3 1.0 + - - -
557Q THR* 3.2 32.7 + - - +
558Q TYR* 4.7 6.8 + - - -
616Q PRO 3.0 18.1 + - - +
617Q ILE 3.7 3.1 - - - +
619Q LEU* 1.3 74.4 - - - +
621Q VAL* 1.3 56.9 + - - +
623Q ALA* 3.4 5.9 + - - +
624Q ASP* 2.9 31.1 + - - +
627Q LYS* 3.9 23.9 + - + +
632Q TRP* 3.8 25.4 - - + -
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Residues in contact with VAL 621 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617Q ILE* 2.9 20.7 + - + +
618Q ASP* 3.7 5.2 - - - +
620Q GLU* 1.3 74.7 - - - +
622Q LEU* 1.3 61.7 + - + +
624Q ASP 3.9 5.4 - - - -
625Q PRO* 2.9 34.8 - - + +
627Q LYS* 5.2 0.4 - - - -
628Q LEU* 4.1 28.3 - - + +
632Q TRP* 3.8 23.3 - - + -
637Q VAL* 4.0 26.7 - - + -
641Q ILE* 5.5 1.8 - - + -
645Q LEU* 3.5 23.7 - - + +
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Residues in contact with LEU 622 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545Q PRO* 3.2 16.3 - - - +
546Q PHE* 3.1 42.4 + - + -
549Q LEU* 3.6 28.7 - - + -
598Q LEU* 3.8 23.1 - - + -
614Q LEU* 4.2 11.7 - - + -
618Q ASP 3.0 22.4 + - - +
619Q LEU* 3.1 5.3 + - - +
621Q VAL* 1.3 76.5 - - - +
623Q ALA* 1.3 57.5 + - - +
625Q PRO* 5.0 0.4 - - - -
641Q ILE* 3.8 28.3 - - + -
644Q VAL* 4.7 6.5 - - + -
645Q LEU* 4.6 18.6 - - + -
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Residues in contact with ALA 623 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544Q ARG* 3.5 30.7 + - - +
546Q PHE 3.6 23.5 + - - +
547Q PRO* 4.3 6.0 - - + +
550Q ALA* 4.0 26.9 - - + +
619Q LEU 3.1 13.7 + - - +
620Q GLU* 3.9 4.9 - - - +
622Q LEU* 1.3 79.0 - - - +
624Q ASP* 1.3 61.6 + - + +
625Q PRO* 3.9 1.3 - - - -
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Residues in contact with ASP 624 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530Q TYR* 5.9 1.4 - - - -
543Q LYS 4.3 5.4 - - - +
544Q ARG* 5.4 3.3 - - + +
620Q GLU 2.9 13.3 + - - +
621Q VAL* 3.1 5.7 - - - +
623Q ALA* 1.3 82.9 - - + +
625Q PRO* 1.3 60.1 - - - +
626Q ASN* 2.8 35.9 + - - +
627Q LYS* 3.0 52.2 + - - +
630Q TYR* 4.2 3.6 + - - -
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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