Contacts of the helix formed by residues 615 - 624 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613P GLU 4.7 3.1 - - - +
614P LEU* 1.3 77.4 - - - +
616P PRO* 1.3 75.6 - - - +
617P ILE* 2.9 21.7 + - - +
618P ASP* 2.7 36.0 + - - +
619P LEU* 3.0 15.4 + - - +
636P ASP 5.1 3.2 + - - +
638P SER* 3.5 10.5 - - - +
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Residues in contact with PRO 616 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553P SER* 3.7 14.3 - - - -
556P ASP* 3.5 43.3 - - + +
557P THR* 5.4 2.5 - - - +
615P THR* 1.3 91.6 - - - +
617P ILE* 1.3 64.7 - - + +
619P LEU* 3.1 7.5 + - + +
620P GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 617 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305P THR* 5.1 10.1 - - - +
306P THR* 5.5 7.4 - - + -
615P THR* 2.9 10.1 + - - +
616P PRO* 1.3 81.7 - - + +
618P ASP* 1.3 64.6 + - - +
620P GLU* 3.1 1.4 + - - +
621P VAL* 2.9 22.2 + - - +
632P TRP* 3.8 57.4 - - + +
636P ASP* 3.4 33.4 - - + +
637P VAL* 3.9 15.9 - - + -
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Residues in contact with ASP 618 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614P LEU* 3.6 19.6 - - + +
615P THR* 2.7 34.9 + - - +
617P ILE* 1.3 79.2 - - - +
619P LEU* 1.3 57.9 + - - +
621P VAL* 3.4 5.7 + - - +
622P LEU* 3.0 34.8 + - - +
636P ASP 4.7 0.2 - - - +
637P VAL* 3.7 11.6 - - - +
638P SER* 2.5 50.2 + - - -
641P ILE* 4.3 12.0 - - + +
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Residues in contact with LEU 619 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549P LEU* 4.1 25.3 - - + +
552P ALA* 3.3 32.5 - - + +
553P SER* 3.8 21.3 - - - +
611P LEU* 4.1 20.2 - - + -
614P LEU* 3.8 33.9 - - + +
615P THR 3.0 13.8 + - - +
616P PRO* 3.1 8.3 + - + +
618P ASP* 1.3 73.3 - - - +
620P GLU* 1.3 66.0 + - - +
622P LEU* 3.1 14.6 + - - +
623P ALA* 3.1 15.0 + - - +
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Residues in contact with GLU 620 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524P ASN* 5.1 2.9 - - - +
550P ALA* 4.1 15.1 - - - +
553P SER* 2.6 27.7 + - - +
554P MET* 4.3 1.2 + - - -
557P THR* 3.2 32.9 + - - +
558P TYR* 4.7 6.9 + - - -
616P PRO 3.0 17.4 + - - +
617P ILE 3.7 3.8 - - - +
619P LEU* 1.3 75.3 - - - +
621P VAL* 1.3 58.4 + - - +
623P ALA* 3.4 5.5 + - - +
624P ASP* 2.9 31.0 + - - +
627P LYS* 3.9 23.3 + - + +
632P TRP* 3.8 26.0 - - + -
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Residues in contact with VAL 621 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617P ILE 2.9 19.1 + - - +
618P ASP* 3.7 6.3 - - - +
620P GLU* 1.3 73.8 - - - +
622P LEU* 1.3 61.4 + - + +
624P ASP 3.9 5.6 - - - -
625P PRO* 2.9 34.7 - - + +
627P LYS* 5.1 0.4 - - + -
628P LEU* 4.1 27.8 - - + +
632P TRP* 3.8 24.5 - - + -
637P VAL* 4.0 25.8 - - + -
641P ILE* 5.5 1.6 - - + -
645P LEU* 3.5 24.0 - - + +
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Residues in contact with LEU 622 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545P PRO* 3.2 16.6 - - - +
546P PHE* 3.1 41.7 + - + -
549P LEU* 3.6 28.0 - - + -
598P LEU* 3.8 23.1 - - + -
614P LEU* 4.2 11.9 - - + -
618P ASP 3.0 22.2 + - - +
619P LEU* 3.1 5.6 + - - +
621P VAL* 1.3 77.0 - - - +
623P ALA* 1.3 58.0 + - - +
641P ILE* 3.8 28.7 - - + -
644P VAL* 4.7 7.0 - - + -
645P LEU* 4.6 19.3 - - + -
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Residues in contact with ALA 623 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544P ARG* 3.5 30.9 + - - +
546P PHE 3.6 24.0 + - - +
547P PRO* 4.3 5.5 - - + +
550P ALA* 4.0 26.7 - - + +
619P LEU 3.1 14.2 + - - +
620P GLU* 3.9 4.9 - - - +
622P LEU* 1.3 77.4 - - - +
624P ASP* 1.3 61.1 + - + +
625P PRO* 3.9 1.6 - - - -
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Residues in contact with ASP 624 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530P TYR* 5.9 1.0 - - - -
543P LYS 4.3 5.4 - - - +
544P ARG* 5.4 2.6 - - + +
620P GLU* 2.9 13.5 + - - +
621P VAL* 3.1 5.6 - - - +
623P ALA* 1.3 82.2 - - + +
625P PRO* 1.3 61.5 - - - +
626P ASN* 2.8 37.0 + - - +
627P LYS* 3.0 53.3 + - + +
630P 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