Contacts of the helix formed by residues 549 - 559 (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 LEU 549 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546P PHE* 3.1 34.6 + - + +
548P GLY* 1.3 70.0 - - - +
550P ALA* 1.3 64.0 + - - +
551P TRP 2.9 5.2 - - - -
552P ALA* 2.8 23.1 + - - +
553P SER* 3.6 3.3 + - - -
591P LEU* 4.2 7.6 - - + -
594P ASP* 4.0 14.6 - - + +
595P THR* 4.0 25.4 - - - +
598P LEU* 4.0 11.9 - - + -
611P LEU* 4.2 13.5 - - + -
619P LEU* 4.1 23.7 - - + +
622P LEU* 3.6 34.8 - - + -
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Residues in contact with ALA 550 (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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525P GLN* 5.7 4.2 - - + +
547P PRO 3.4 13.9 + - - +
548P GLY 3.2 1.0 - - - -
549P LEU* 1.3 76.8 - - - +
551P TRP* 1.3 61.9 + - - +
552P ALA 3.2 0.2 - - - -
553P SER* 3.4 12.3 + - - +
554P MET* 3.0 23.2 + - - +
587P ARG* 4.8 7.4 - - - +
619P LEU 5.0 2.0 - - - -
620P GLU* 4.1 11.9 - - - +
623P ALA* 4.0 18.9 - - + +
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Residues in contact with TRP 551 (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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525P GLN* 4.0 7.9 - - - -
548P GLY 3.3 15.9 + - - +
549P LEU 2.8 0.8 + - - -
550P ALA* 1.3 79.3 - - - +
552P ALA* 1.3 61.8 + - - +
554P MET* 3.3 58.5 + - + +
555P LYS* 4.5 1.7 + - - +
568P LEU* 4.1 12.3 - - + -
583P TYR* 3.7 24.7 - + - -
584P ARG* 4.2 24.9 - - + -
587P ARG* 3.4 56.8 - - + +
588P GLU* 3.6 22.5 + - + -
591P LEU* 3.9 20.0 - - + -
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Residues in contact with ALA 552 (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 2.8 8.0 + - - +
551P TRP* 1.3 80.7 - - - +
553P SER* 1.3 57.9 + - - +
554P MET 3.6 0.2 + - - -
555P LYS* 4.6 6.4 + - - +
556P ASP* 5.0 3.5 + - - +
591P LEU* 4.1 14.3 - - + +
611P LEU* 4.1 19.7 - - + -
619P LEU* 3.3 25.5 - - + +
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Residues in contact with SER 553 (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 3.6 0.6 + - - -
550P ALA* 3.4 12.0 + - - -
551P TRP 3.3 0.2 - - - -
552P ALA* 1.3 77.7 - - - +
554P MET* 1.3 53.4 + - - +
555P LYS 3.5 0.7 - - - -
556P ASP* 3.2 9.6 + - - +
557P THR* 2.7 36.3 + - - -
616P PRO* 3.7 29.6 - - - -
619P LEU* 3.8 13.8 - - - +
620P GLU* 2.6 32.6 + - - +
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Residues in contact with MET 554 (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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521P MET* 3.6 24.5 - - - +
525P GLN* 3.4 24.9 - - - +
550P ALA 3.0 12.7 + - - +
551P TRP* 3.3 56.3 - - + +
552P ALA 3.3 1.8 - - - -
553P SER* 1.3 77.7 - - - +
555P LYS* 1.3 56.7 + - + +
557P THR* 4.6 0.4 - - - -
558P TYR* 2.7 44.5 + - + +
559P GLY 3.8 0.2 + - - -
564P TYR* 3.3 18.8 + - + +
568P LEU* 3.8 16.4 - - + -
620P GLU* 4.7 1.3 - - - -
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Residues in contact with LYS 555 (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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551P TRP 4.5 2.2 + - - -
552P ALA 4.6 4.5 + - - +
553P SER 3.5 0.6 - - - -
554P MET* 1.3 78.7 - - + +
556P ASP* 1.3 57.6 + - - +
559P GLY* 2.6 40.5 + - - -
564P TYR* 3.0 45.7 + - + +
565P SER* 5.7 1.0 + - - -
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Residues in contact with ASP 556 (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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307P ARG* 5.0 12.0 + - - -
552P ALA 5.1 1.8 - - - +
553P SER* 3.2 12.7 + - - +
554P MET 3.1 0.2 - - - -
555P LYS* 1.3 85.0 - - - +
557P THR* 1.3 65.7 + - - +
559P GLY* 4.2 1.9 + - - -
560P ALA* 5.2 2.4 + - - +
616P PRO* 3.5 36.9 - - + +
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Residues in contact with THR 557 (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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307P ARG* 4.3 9.1 - - - +
499P ASP* 5.1 0.5 - - - +
516P GLY* 4.0 17.8 + - - -
553P SER* 2.7 19.4 + - - -
556P ASP* 1.3 78.4 + - - +
558P TYR* 1.3 96.9 + - + +
560P ALA 5.4 0.5 + - - -
616P PRO* 5.4 1.9 - - - +
620P GLU* 3.2 30.9 + - - +
631P LYS* 6.3 2.9 - - - -
632P TRP* 5.7 1.3 - - + -
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Residues in contact with TYR 558 (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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516P GLY* 4.7 3.6 - - - -
517P ASN 3.2 37.7 - - - -
518P ILE* 4.5 5.8 - - + -
520P SER* 3.7 7.6 + - - -
521P MET* 3.4 49.2 + - + -
524P ASN* 3.6 19.8 + - - +
554P MET* 2.7 27.6 + - + +
557P THR* 1.3 98.8 - - + +
559P GLY* 1.3 64.7 + - - +
560P ALA* 3.1 3.8 - - - -
561P CYS* 2.8 23.7 + - + +
564P TYR* 3.7 19.4 - - + -
620P GLU* 4.7 10.0 + - - -
627P LYS* 5.7 1.9 - - - -
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Residues in contact with GLY 559 (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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554P MET 3.8 0.6 + - - -
555P LYS* 2.6 40.9 + - - -
556P ASP 4.2 0.2 + - - -
557P THR 3.8 0.6 - - - -
558P TYR* 1.3 71.3 - - - +
560P ALA* 1.3 61.6 + - - +
561P CYS 3.1 9.2 + - - +
564P TYR* 3.7 28.1 - - - +
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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