Contacts of the helix formed by residues 551 - 563 (chain V) in PDB entry 1I84
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 551 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549V LYS 5.9 0.2 - - - -
550V ALA* 1.3 74.7 - - - +
552V ASP* 1.3 62.0 + - - +
553V THR* 3.4 14.7 + - - -
554V SER* 2.3 66.3 + - - -
555V PHE 2.6 4.0 + - - -
598V LEU* 3.8 7.9 - - - -
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Residues in contact with ASP 552 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551V THR* 1.3 71.5 - - - +
553V THR* 1.3 64.6 + - - +
555V PHE* 2.9 19.9 - - - +
556V VAL* 2.9 21.5 - - - +
579V THR* 5.2 2.2 - - - +
594V ALA 3.5 14.9 - - - +
595V SER* 3.8 9.1 - - - +
596V ALA* 3.0 25.2 + - - -
597V TRP* 2.8 21.7 + - - +
598V LEU* 3.1 22.5 + - - +
599V THR* 4.9 1.4 + - - -
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Residues in contact with THR 553 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551V THR* 2.6 17.5 + - - -
552V ASP* 1.3 70.4 - - - +
554V SER* 1.3 69.7 + - - -
555V PHE 2.7 1.9 + - - -
556V VAL 2.8 11.4 + - - -
557V GLU* 2.4 37.4 - - + +
576V LYS 4.0 5.4 - - - +
577V ASP 5.6 0.9 - - - +
579V THR* 3.2 29.5 + - + +
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Residues in contact with SER 554 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544V GLU* 3.1 15.4 + - - +
549V LYS 4.5 4.5 - - - -
550V ALA* 3.0 14.0 - - - -
551V THR* 2.3 48.9 + - - -
553V THR* 1.3 75.9 - - - +
555V PHE* 1.3 68.9 + - - +
557V GLU* 3.4 11.5 - - - +
558V LYS* 3.1 18.0 + - - +
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Residues in contact with PHE 555 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537V VAL* 3.8 11.9 - - + -
540V LEU* 3.7 8.3 - - + -
541V LEU* 3.2 63.5 - - + -
544V GLU* 4.0 17.9 - - + +
551V THR 2.6 12.0 + - - +
552V ASP* 2.9 19.7 - - - +
553V THR 2.7 1.4 + - - -
554V SER* 1.3 70.8 + - - +
556V VAL* 1.3 62.9 + - - +
558V LYS* 2.7 11.7 + - - +
559V LEU* 2.6 64.5 + - + -
581V PHE* 4.4 4.5 - + - -
594V ALA* 3.9 16.6 - - + -
597V TRP* 3.9 14.1 - + - -
598V LEU* 4.7 4.3 - - + -
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Residues in contact with VAL 556 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552V ASP 2.9 17.5 - - - +
553V THR 2.8 6.2 + - - +
555V PHE* 1.3 74.0 - - - +
557V GLU* 1.3 55.5 + - - +
559V LEU* 2.7 30.9 + - + +
560V ILE* 2.7 38.8 + - + +
576V LYS* 6.1 0.9 - - + -
579V THR* 3.7 27.4 - - + -
580V GLU 4.5 15.5 - - - +
581V PHE* 4.6 10.8 - - + -
594V ALA* 3.4 25.8 - - + -
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Residues in contact with GLU 557 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553V THR* 2.4 51.9 - - - +
554V SER* 3.4 11.9 - - - +
556V VAL* 1.3 72.9 - - - +
558V LYS* 1.3 62.9 + - - +
560V ILE* 3.0 24.0 - - - +
561V GLN* 3.0 10.0 + - - +
576V LYS* 4.8 7.6 - - - +
579V THR* 3.0 15.0 - - - +
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Residues in contact with LYS 558 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540V LEU* 5.0 12.8 - - + -
543V GLU* 4.0 19.4 + - - +
544V GLU* 3.5 34.0 + - + +
547V PHE* 6.0 2.8 - - - -
554V SER 3.1 7.9 + - - +
555V PHE* 2.7 15.9 + - + +
557V GLU* 1.3 72.0 - - - +
559V LEU* 1.3 57.2 + - - +
561V GLN* 2.5 72.2 + - + +
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Residues in contact with LEU 559 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537V VAL* 3.9 18.8 - - + -
540V LEU* 3.4 26.8 - - + +
555V PHE* 2.6 39.1 + - + +
556V VAL* 2.7 24.1 + - + +
558V LYS* 1.3 73.9 - - - +
560V ILE* 1.3 59.6 + - - -
561V GLN 3.2 0.2 + - - -
562V GLU* 3.4 0.9 + - - +
563V GLN* 3.3 24.9 + - + +
564V GLY 3.7 2.3 + - - -
569V PHE* 3.7 15.0 - - + -
581V PHE* 3.2 50.9 - - + -
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Residues in contact with ILE 560 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556V VAL* 2.7 43.4 + - + +
557V GLU* 3.0 20.4 - - - +
559V LEU* 1.3 75.2 - - + +
561V GLN* 1.3 63.5 + - - +
564V GLY* 2.9 33.6 - - - +
569V PHE* 4.7 20.9 - - + -
571V LYS* 5.2 15.7 - - + -
580V GLU 5.8 1.1 - - - +
581V PHE* 5.6 0.7 - - + -
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Residues in contact with GLN 561 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540V LEU* 4.7 1.4 - - - +
557V GLU 3.0 8.0 + - - +
558V LYS* 2.5 69.8 + - + +
560V ILE* 1.3 73.3 - - - +
562V GLU* 1.3 106.7 + - - +
564V GLY* 4.8 0.3 - - - -
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Residues in contact with GLU 562 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534V PRO* 5.1 2.3 - - - +
535V PRO* 3.7 36.8 - - + +
540V LEU* 4.0 12.3 - - + -
558V LYS 3.1 1.6 + - - -
559V LEU 4.1 2.7 - - - +
561V GLN* 1.3 119.3 + - - +
563V GLN* 1.3 88.1 + - - +
565V ASN* 5.4 0.5 + - - -
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Residues in contact with GLN 563 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527V LEU* 3.6 35.7 - - + +
534V PRO* 4.9 8.8 - - - +
535V PRO 2.7 32.3 + - - +
536V GLY* 4.4 2.6 - - - -
537V VAL* 5.0 3.1 - - + -
540V LEU* 4.3 8.3 - - - +
559V LEU* 3.3 11.4 + - + +
562V GLU* 1.3 96.8 - - - +
564V GLY* 1.3 56.2 + - - +
565V ASN* 2.5 27.0 + - - -
566V HIS* 3.2 31.2 + - + -
569V PHE* 4.2 13.9 - - + -
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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