Contacts of the strand formed by residues 546 - 554 (chain C) in PDB entry 4QG0
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 ALA 546 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.0 5.3 - - - +
505C MET 3.3 6.3 - - - +
506C ASP* 3.9 8.5 - - + +
510C GLN* 3.2 29.8 - - - +
511C GLU* 4.2 8.0 - - + +
544C LYS* 3.6 22.6 + - - +
545C PHE* 1.3 76.0 - - - +
547C GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 547 (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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538A SER* 2.8 25.7 + - - -
539A GLN* 2.7 34.2 + - + +
540A LEU* 3.6 22.6 - - + +
367C ASN* 5.1 2.8 + - - +
461C GLN* 2.9 22.2 + - - +
504C ASN* 3.8 1.6 - - - +
505C MET* 2.9 48.5 + - + +
544C LYS* 5.3 2.0 - - - +
546C ALA* 1.3 76.5 - - - +
548C GLN* 1.3 72.2 + - - +
549C LEU* 5.1 6.3 - - + +
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Residues in contact with GLN 548 (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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461C GLN* 3.0 25.7 + - - +
462C PRO* 3.6 23.1 - - + +
466C ILE 4.7 0.7 - - - +
467C LYS* 3.8 11.6 - - + +
468C ILE* 3.0 51.0 + - - +
473C TYR* 4.7 0.2 + - - -
502C VAL* 3.9 12.0 - - + +
503C ILE 3.3 5.6 - - - +
504C ASN* 2.6 32.3 + - - +
547C GLU* 1.3 80.9 - - - +
549C LEU* 1.3 65.5 + - - +
550C ILE* 4.8 3.4 - - + -
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Residues in contact with LEU 549 (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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537A VAL 4.7 8.7 - - - +
371C ARG* 6.4 3.4 - - + -
375C GLN* 5.9 0.2 - - + -
459C GLU* 3.8 34.3 - - - +
460C THR 3.9 1.8 - - - -
461C GLN* 3.9 28.0 - - + +
501C ASP 3.7 0.9 - - - +
502C VAL* 3.5 0.7 - - - +
503C ILE* 2.9 40.1 + - + +
505C MET* 3.8 33.9 - - + -
547C GLU* 5.1 6.7 - - + +
548C GLN* 1.3 74.6 - - - +
550C ILE* 1.3 68.6 + - - +
551C ARG* 4.1 20.6 - - - +
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Residues in contact with ILE 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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458C GLY 3.8 0.2 - - - +
459C GLU* 3.2 4.8 - - - +
460C THR* 2.9 51.2 + - + +
462C PRO* 4.3 18.2 - - + -
468C ILE* 4.3 17.5 - - + -
476C LEU* 5.4 1.1 - - + -
500C VAL* 3.7 28.3 - - + -
501C ASP 3.5 2.7 - - - +
502C VAL* 3.6 26.9 - - + -
548C GLN* 4.8 2.0 - - + -
549C LEU* 1.3 86.8 - - - +
551C ARG* 1.3 64.3 + - - +
552C VAL* 4.1 1.3 + - + -
569C PHE* 5.0 0.9 - - - -
572C TRP* 4.1 21.5 - - + -
578C PHE* 5.1 5.8 - - + -
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Residues in contact with ARG 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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371C ARG* 5.1 8.7 + - - +
375C GLN* 2.6 37.1 + - - +
377C LYS* 4.1 14.3 - - + +
380C ASN* 3.6 16.2 - - - +
456C TYR* 4.0 18.2 - - + -
458C GLY 3.3 3.6 - - - +
459C GLU* 2.5 32.4 + - + +
499C ILE 3.7 1.0 - - - +
500C VAL* 3.5 4.3 - - - +
501C ASP* 2.9 41.8 + - + +
503C ILE* 4.1 21.3 - - - +
549C LEU* 4.1 17.5 - - - +
550C ILE* 1.3 74.6 - - - +
552C VAL* 1.3 63.0 + - - +
553C TYR* 4.0 25.0 + - + +
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Residues in contact with VAL 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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456C TYR* 3.9 2.1 - - - -
457C VAL* 2.9 36.8 + - + +
458C GLY 2.9 17.4 + - - +
480C VAL* 4.8 4.3 - - + -
498C PHE* 4.2 17.3 - - + -
499C ILE 3.3 8.1 - - - +
500C VAL* 4.3 14.1 - - + -
550C ILE* 4.7 2.2 - - + -
551C ARG* 1.3 78.9 - - - +
553C TYR* 1.3 72.2 + - - +
569C PHE* 3.5 42.4 - - + -
572C TRP* 4.1 17.5 - - + -
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Residues in contact with TYR 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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377C LYS* 2.9 36.8 + - - -
378C VAL* 5.5 0.2 - - - -
380C ASN* 4.1 10.3 - - - +
381C ILE* 3.7 38.1 - - + -
454C PHE* 4.5 7.9 - - + -
455C LYS 3.1 9.6 - - - +
456C TYR* 3.6 38.1 - + + -
457C VAL* 3.6 4.5 - - - -
498C PHE* 3.5 5.7 - - - -
499C ILE* 2.9 48.0 + - + +
501C ASP* 4.2 17.3 + - + -
551C ARG* 4.0 29.3 + - + +
552C VAL* 1.3 78.0 - - - +
554C CYS* 1.3 61.1 + - - +
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Residues in contact with CYS 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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454C PHE* 4.4 2.2 - - - -
455C LYS* 2.7 36.7 + - - +
457C VAL* 3.8 4.9 - - + +
493C LEU* 4.3 14.8 - - - -
497C ASP 3.2 11.0 - - - +
498C PHE* 4.9 3.4 - - + -
553C TYR* 1.3 73.7 - - - +
555C LYS* 1.3 62.0 + - - +
556C LYS* 3.2 38.9 + - - +
561C SER 4.5 2.2 - - - -
562C LEU* 4.9 5.6 - - + -
565C ALA* 3.9 30.1 - - + -
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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