Contacts of the helix formed by residues 555 - 565 (chain C) in PDB entry 1Z5S
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 555 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C PHE* 4.0 17.7 - - + -
509C SER* 4.0 31.0 - - - +
510C ASN* 4.0 25.4 - - - +
512C PHE* 5.5 1.6 - - + -
513C LEU* 4.3 21.2 - - + +
551C PHE* 4.0 27.8 - - + -
552C PRO* 3.0 27.5 + - + +
554C ALA* 1.3 78.9 - - + +
556C ALA* 1.3 67.4 + - - +
557C PRO* 3.5 0.7 - - - -
558C LEU* 3.2 13.5 + - + +
559C LEU* 3.2 20.3 + - - +
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Residues in contact with ALA 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C PHE* 4.4 9.4 - - + -
552C PRO 4.1 1.4 + - - -
553C LYS* 3.3 23.4 + - + +
554C ALA 2.9 2.4 - - - -
555C LEU* 1.3 77.1 - - - +
557C PRO* 1.3 70.7 - - + +
559C LEU* 3.3 4.5 + - - +
560C LEU* 3.1 21.0 + - - +
584C LEU* 4.3 9.7 - - - +
587C VAL* 4.3 27.4 - - + +
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Residues in contact with PRO 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.9 13.0 - - + +
139A GLN* 4.4 15.7 - - + +
553C LYS 4.6 1.1 - - - +
554C ALA* 3.4 11.2 - - - +
556C ALA* 1.3 96.8 - - + +
558C LEU* 1.3 68.2 + - + +
560C LEU* 3.4 15.8 - - + +
561C ALA* 2.8 36.4 + - - +
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Residues in contact with LEU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 4.9 5.2 - - + +
132A GLU* 4.8 21.8 - - - +
135A THR* 3.6 29.6 - - + +
136A ILE* 5.7 4.0 - - + -
139A GLN* 5.7 0.4 - - - +
510C ASN* 4.0 21.1 - - + +
513C LEU* 3.8 24.7 - - + -
517C LEU* 4.0 5.0 - - - +
554C ALA 4.2 8.7 - - - +
555C LEU* 3.2 15.4 + - + +
557C PRO* 1.3 95.1 - - + +
559C LEU* 1.3 60.0 + - - +
561C ALA* 4.0 0.8 - - - +
562C PHE* 3.6 27.4 + - - +
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Residues in contact with LEU 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C LEU* 3.8 17.9 - - + +
516C LEU* 5.4 1.6 - - + -
517C LEU* 4.2 17.3 - - + -
520C MET* 6.2 0.2 - - - -
522C LEU* 5.8 0.7 - - + -
542C LEU* 4.1 33.9 - - + -
546C VAL* 4.1 24.7 - - + -
551C PHE* 4.9 11.0 - - + -
555C LEU 3.2 11.5 + - - +
556C ALA 3.7 7.2 - - - +
557C PRO 3.2 0.2 - - - -
558C LEU* 1.3 73.7 - - - +
560C LEU* 1.3 68.5 + - - +
561C ALA 3.1 1.6 - - - -
562C PHE* 3.0 2.8 + - - -
563C VAL* 2.9 55.5 + - + +
580C LEU* 4.7 2.2 - - + -
584C LEU* 4.2 12.3 - - + -
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Residues in contact with LEU 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C ALA 3.1 11.7 + - - +
557C PRO* 3.4 17.9 - - + +
559C LEU* 1.3 79.7 - - - +
561C ALA* 1.3 52.7 - - - +
563C VAL* 3.5 1.6 + - - +
564C THR* 2.5 39.7 + - + +
581C LEU* 3.9 9.9 - - + -
584C LEU* 3.8 26.3 - - + +
585C TYR* 3.5 39.0 - - + -
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Residues in contact with ALA 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 4.0 17.3 + - + -
135A THR* 4.0 31.0 - - + +
138A CYS* 6.0 3.1 - - + -
557C PRO 2.8 17.7 + - - +
558C LEU 4.1 2.5 - - - +
560C LEU* 1.3 79.3 - - - +
562C PHE* 1.3 59.9 + - + +
564C THR* 3.1 14.7 + - - -
565C LYS* 3.1 16.3 + - - +
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Residues in contact with PHE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.7 19.1 - - + -
131A ALA* 3.7 25.6 - - + -
134A TYR* 3.3 32.3 - + - -
135A THR* 4.9 0.4 - - - -
517C LEU* 3.4 37.7 - - + -
522C LEU* 3.1 54.7 - - + +
523C LEU* 3.6 26.2 - - + -
558C LEU 3.6 10.8 + - - +
559C LEU 3.0 4.4 + - - +
561C ALA* 1.3 79.6 - - + +
563C VAL* 1.3 60.2 + - - +
565C LYS* 3.7 20.2 - - + +
570C LEU* 3.4 5.9 - - - +
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Residues in contact with VAL 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522C LEU* 5.2 3.4 - - + -
539C LEU* 4.2 9.6 - - + -
542C LEU* 5.6 0.4 - - + -
559C LEU* 2.9 46.3 + - + +
560C LEU 4.1 3.1 - - - +
562C PHE* 1.3 77.8 - - - +
564C THR* 1.3 57.7 + - - +
565C LYS 3.1 1.8 - - - -
570C LEU* 2.8 26.2 - - + +
577C ARG* 2.7 53.3 + - + +
580C LEU* 4.0 17.0 - - + -
581C LEU* 3.9 15.7 - - + -
584C LEU* 4.5 3.8 - - + -
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Residues in contact with THR 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C LEU* 2.5 28.7 + - + +
561C ALA* 3.1 12.6 + - - -
563C VAL* 1.3 73.4 - - - +
565C LYS* 1.3 61.8 + - - +
566C PRO* 2.9 11.5 - - - +
577C ARG* 2.8 20.1 + - - +
581C LEU* 3.4 28.0 - - + -
585C TYR* 4.0 12.3 - - + +
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Residues in contact with LYS 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE 4.5 4.9 - - - -
126A GLN* 4.9 13.9 + - - +
127A ASP* 4.8 2.8 - - - +
128A PRO* 3.7 28.3 - - - +
134A TYR* 3.0 34.5 - - + +
522C LEU* 4.1 15.9 + - + +
523C LEU* 6.0 0.2 - - - +
561C ALA 3.1 18.0 + - - +
562C PHE* 3.7 24.1 - - + +
563C VAL 3.1 0.4 - - - +
564C THR* 1.3 76.4 - - - +
566C PRO* 1.3 85.8 + - + +
567C ASN* 3.0 14.1 + - + +
570C LEU* 3.9 9.4 - - - +
577C ARG* 4.2 0.9 + - - -
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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