Contacts of the strand formed by residues 555 - 564 (chain C) in PDB entry 4P3N
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 TYR 555 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493C SER* 4.8 1.7 + - - -
494C PHE* 5.4 0.9 - - - -
495C LYS* 3.8 40.1 - - + +
547C GLN* 4.2 29.4 + - + +
548C ILE 3.2 17.0 - - - -
549C LYS* 3.5 41.5 - - + +
553C GLY 3.9 14.1 - - - -
554C ARG* 1.3 78.3 - - - +
556C HIS* 1.3 71.7 + - - +
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Residues in contact with HIS 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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547C GLN* 3.2 6.4 - - - +
548C ILE* 2.9 46.5 + - + +
550C ASP* 2.9 33.5 + - + +
554C ARG* 3.7 20.6 + - + -
555C TYR* 1.3 83.4 + - - +
557C GLN* 1.3 62.1 + - - +
558C CYS* 3.4 2.1 + - - -
599C ARG* 4.1 15.2 + - - +
603C ILE* 3.9 44.4 - - + +
606C GLU* 5.7 5.2 - - - -
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Residues in contact with GLN 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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497C ASN* 4.5 2.8 + - - +
545C ASP* 3.5 40.5 + - - +
546C ILE 3.9 6.2 + - - +
547C GLN* 3.3 36.3 - - + +
556C HIS* 1.3 71.0 - - - +
558C CYS* 1.3 59.9 + - - +
559C ALA 4.7 6.1 - - - +
560C THR* 6.4 0.2 - - - -
599C ARG* 2.9 22.5 + - - +
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Residues in contact with CYS 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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487C TYR* 3.8 7.6 - - - +
546C ILE 3.5 3.0 + - - +
548C ILE* 3.8 20.2 - - + -
556C HIS 3.4 3.4 + - - +
557C GLN* 1.3 78.1 - - - +
559C ALA* 1.3 63.6 + - - +
560C THR* 4.0 2.3 + - - +
592C ALA* 4.3 3.5 - - - +
593C ILE 3.2 17.9 - - - +
594C LEU 4.1 9.2 - - - +
595C GLY* 3.7 22.5 + - - +
599C ARG* 4.1 8.1 - - - +
600C MET* 3.8 26.7 - - - -
603C ILE* 3.9 15.7 - - - -
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Residues in contact with ALA 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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483C LEU* 4.4 8.7 - - + -
487C TYR* 3.3 21.5 - - - +
545C ASP* 3.8 3.1 - - - +
546C ILE* 3.1 51.2 + - + +
557C GLN* 4.7 4.0 - - - +
558C CYS* 1.3 77.4 - - - +
560C THR* 1.3 63.4 + - - +
592C ALA 3.2 14.6 - - - +
593C ILE* 4.0 3.8 - - - +
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Residues in contact with THR 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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543C LYS* 4.4 7.3 + - - +
544C ILE 3.4 7.4 + - - -
545C ASP* 2.9 20.4 + - - -
546C ILE* 4.3 0.4 - - - -
557C GLN* 6.4 0.2 - - - -
558C CYS 4.0 1.9 + - - +
559C ALA* 1.3 76.9 - - - +
561C ILE* 1.3 73.0 + - - +
562C GLN* 4.4 10.3 + - + +
590C HIS* 5.1 1.8 - - + +
591C ARG* 3.2 8.5 - - - +
592C ALA* 3.2 34.0 + - + +
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Residues in contact with ILE 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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476C ILE* 4.0 24.0 - - + -
479C CYS* 3.6 30.1 - - + -
480C LEU* 4.1 23.1 - - + -
483C LEU* 4.7 5.6 - - + -
519C LEU* 6.0 0.4 - - + -
543C LYS* 3.3 4.7 - - - +
544C ILE* 2.9 49.8 + - + +
546C ILE* 4.1 9.6 - - + -
560C THR* 1.3 77.9 - - - +
562C GLN* 1.3 59.7 + - - +
563C LEU* 4.1 3.2 + - + +
589C VAL* 3.7 24.2 - - + -
590C HIS 3.7 1.8 - - - -
591C ARG* 4.2 9.2 - - + -
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Residues in contact with GLN 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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538C ALA* 3.6 19.4 - - - +
540C TYR* 3.3 38.6 + - + +
541C GLY 3.8 10.7 + - - -
542C PRO 4.0 0.2 - - - -
543C LYS* 2.4 48.0 - - - +
560C THR* 4.0 10.7 + - + +
561C ILE* 1.3 74.6 - - - +
563C LEU* 1.3 68.4 + - - +
589C VAL* 3.5 1.6 - - - -
590C HIS* 2.8 51.8 + - + +
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Residues in contact with LEU 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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472C ILE* 4.0 26.7 - - + -
476C ILE* 4.3 14.4 - - + -
515C ALA* 3.9 27.6 - - + -
519C LEU* 4.5 9.9 - - + -
540C TYR* 3.5 8.1 - - - +
541C GLY* 3.2 22.7 + - - -
542C PRO* 3.0 34.0 + - + +
561C ILE* 4.1 2.9 + - + +
562C GLN* 1.3 76.9 - - - +
564C ASP* 1.3 59.8 + - - +
565C PHE* 4.3 4.5 - - + -
587C VAL* 4.0 10.3 - - + -
588C ILE 3.6 2.0 - - - +
589C VAL* 3.7 32.8 - - + -
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Residues in contact with ASP 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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540C TYR* 3.3 19.8 - - + +
563C LEU* 1.3 74.8 - - - +
565C PHE* 1.3 62.3 + - - +
566C GLN* 2.8 36.1 + - - +
567C LEU* 3.0 30.4 + - - +
568C PRO* 3.6 7.0 - - - +
587C VAL* 4.0 3.0 - - - +
588C ILE* 2.8 38.8 + - + +
590C HIS* 2.9 34.7 + - + +
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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