Contacts of the helix formed by residues 549 - 559 (chain C) in PDB entry 5ZR1
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 PRO 549 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513C LEU* 4.1 13.5 - - + -
516C ILE* 3.7 40.4 - - + +
517C MET* 4.5 9.6 - - + -
547C THR 4.0 4.7 - - - +
548C LEU* 1.3 86.0 - - + +
550C LYS* 1.3 65.3 + - - +
551C GLU 3.5 0.2 - - - -
552C GLU* 3.9 19.3 - - + +
553C ILE* 3.3 26.0 + - + +
576C PHE* 4.2 0.7 - - - -
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Residues in contact with LYS 550 (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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548C LEU 3.6 3.4 + - - +
549C PRO* 1.3 74.1 - - - +
551C GLU* 1.3 82.1 + - + +
553C ILE 3.9 0.2 + - - -
554C LEU* 3.5 47.9 + - + +
573C PRO 5.4 6.5 + - - -
576C PHE* 3.6 45.0 - - + +
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Residues in contact with GLU 551 (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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549C PRO 3.5 0.4 - - - -
550C LYS* 1.3 97.9 - - + +
552C GLU* 1.3 72.2 + - - +
554C LEU* 3.6 5.8 + - - +
555C ASN* 2.9 26.4 + - - +
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Residues in contact with GLU 552 (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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512C ASP* 5.0 10.8 - - + +
513C LEU* 4.0 12.5 - - + +
516C ILE* 3.7 28.4 - - + +
549C PRO* 3.9 14.8 + - + +
551C GLU* 1.3 87.6 + - - +
553C ILE* 1.3 61.4 + - - +
555C ASN* 3.6 15.1 - - + +
556C PHE* 2.9 27.9 + - - +
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Residues in contact with ILE 553 (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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281B PHE* 4.0 11.2 - - + -
513C LEU* 4.1 18.8 - - + -
517C MET* 4.2 16.8 - - + -
548C LEU* 3.7 33.7 - - + -
549C PRO* 3.3 22.7 + - + +
550C LYS 4.4 2.2 - - - +
551C GLU 3.5 0.6 - - - -
552C GLU* 1.3 77.4 - - - +
554C LEU* 1.3 61.6 + - + +
556C PHE* 3.2 7.0 + - - +
557C ILE* 2.8 29.5 + - + +
576C PHE* 3.9 17.3 - - + -
579C VAL* 3.8 29.4 - - + -
580C ALA* 6.4 0.2 - - - -
583C LEU* 5.4 3.6 - - + -
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Residues in contact with LEU 554 (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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550C LYS* 3.5 42.6 + - - +
551C GLU* 4.0 5.4 - - - +
553C ILE* 1.3 79.6 - - + +
555C ASN* 1.3 62.0 + - - +
557C ILE* 3.4 19.6 - - + +
558C ARG* 3.2 49.0 + - - +
570C ALA* 5.3 0.2 - - - -
572C THR 6.0 0.2 - - - +
575C ALA* 3.7 31.2 - - + +
576C PHE* 3.8 21.1 - - + +
579C VAL* 5.1 3.1 - - + -
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Residues in contact with ASN 555 (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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512C ASP* 5.9 0.4 + - - -
551C GLU 2.9 19.0 + - - +
552C GLU* 3.8 16.5 - - + +
553C ILE 3.2 0.2 - - - -
554C LEU* 1.3 76.9 - - - +
556C PHE* 1.3 62.6 + - - +
558C ARG* 3.4 7.9 + - - +
559C LYS* 3.1 36.9 + - - +
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Residues in contact with PHE 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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280B PHE* 3.4 38.6 - + - -
281B PHE* 3.5 37.5 - + - -
284B ASN* 3.6 33.0 - - + -
285B PHE* 4.0 2.2 - - - -
509C LEU* 3.6 27.6 - - + +
510C SER* 3.5 22.4 - - - -
513C LEU* 3.6 27.1 - - + -
552C GLU 2.9 19.0 + - - +
553C ILE 3.2 2.4 + - - +
555C ASN* 1.3 76.2 - - - +
557C ILE* 1.3 62.7 + - - +
558C ARG 3.3 0.5 + - - -
559C LYS* 3.4 15.6 + - - +
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Residues in contact with ILE 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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277B VAL* 4.7 7.6 - - + -
280B PHE* 3.6 28.1 - - + -
281B PHE* 4.0 20.6 - - + -
553C ILE* 2.8 12.9 + - + +
554C LEU* 3.4 31.0 - - + +
556C PHE* 1.3 77.6 - - + +
558C ARG* 1.3 60.0 + - - +
560C ASP 4.6 4.3 + - - +
566C LEU* 3.7 45.9 - - + +
567C LEU* 4.3 6.6 - - - +
569C LEU* 5.5 2.7 - - + -
570C ALA* 3.7 22.7 - - + -
579C VAL* 4.8 12.1 - - + -
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Residues in contact with ARG 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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554C LEU* 3.2 52.4 + - - +
555C ASN* 3.4 9.0 + - - +
556C PHE 3.2 0.4 - - - -
557C ILE* 1.3 77.6 - - - +
559C LYS* 1.3 62.1 + - - +
560C ASP 3.2 12.6 + - - +
561C PRO* 4.4 1.4 - - - +
567C LEU* 3.8 18.7 - - + +
570C ALA* 2.5 49.4 + - + +
571C GLU* 4.3 4.8 - - - +
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Residues in contact with LYS 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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508C THR 4.7 5.3 + - - +
509C LEU* 3.4 51.2 + - + +
512C ASP* 3.5 30.5 + - - +
555C ASN* 3.1 32.2 + - - +
556C PHE* 3.4 10.3 + - - +
558C ARG* 1.3 75.7 - - - +
560C ASP* 1.3 57.0 + - - +
561C PRO* 3.3 12.0 - - - +
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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