Contacts of the strand formed by residues 587 - 596 (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 VAL 587 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C ILE 3.3 12.5 - - - +
466C PHE* 3.9 1.4 - - - -
467C CYS* 2.9 25.4 + - - +
469C MET* 3.9 39.3 - - + +
472C ILE* 4.0 22.2 - - + -
511C VAL* 5.6 1.3 - - + -
563C LEU* 4.0 7.9 - - + -
564C ASP 4.0 3.8 - - - +
565C PHE* 3.7 31.6 - - + -
568C PRO* 4.6 0.2 - - - -
585C ARG 5.3 1.6 - - - +
586C PRO* 1.3 77.6 - - - +
588C ILE* 1.3 72.9 + - - +
589C VAL* 4.7 0.2 - - + -
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Residues in contact with ILE 588 (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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417C CYS* 3.6 31.4 - - - -
464C HIS* 4.2 13.5 - - + -
465C ILE 3.6 3.8 - - - +
466C PHE* 3.9 26.2 - - + -
563C LEU* 3.6 3.3 - - - -
564C ASP* 2.8 43.5 + - + +
567C LEU* 3.6 17.7 - - + -
568C PRO* 3.8 12.1 - - + +
573C LEU* 4.0 7.6 - - + -
586C PRO* 5.6 0.7 - - + -
587C VAL* 1.3 76.1 - - - +
589C VAL* 1.3 67.5 + - - +
590C HIS* 3.8 29.6 - - + +
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Residues in contact with VAL 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ALA 3.4 1.2 - - - +
464C HIS* 3.2 4.9 - - - -
465C ILE* 2.9 59.2 + - + +
467C CYS* 4.4 3.8 - - - -
472C ILE* 4.2 18.4 - - + -
475C GLU* 6.0 1.8 - - + -
476C ILE* 4.5 6.7 - - + -
479C CYS* 5.2 0.2 - - - -
561C ILE* 3.7 20.4 - - + -
562C GLN 3.5 2.7 - - - +
563C LEU* 3.7 28.9 - - + -
587C VAL* 4.4 3.1 - - + +
588C ILE* 1.3 82.4 - - - +
590C HIS* 1.3 73.2 + - - +
591C ARG* 4.7 2.9 - - + -
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Residues in contact with HIS 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C MET* 5.9 0.9 - - - -
413C CYS* 3.2 25.9 - - + -
462C ASP* 5.3 2.7 - - - +
464C HIS* 3.0 29.9 + + + +
540C TYR* 5.0 3.4 - + - -
560C THR* 5.5 1.8 - - + -
562C GLN* 2.8 55.2 + - + +
564C ASP* 2.9 40.5 + - + +
567C LEU* 3.5 20.1 - - + +
588C ILE* 3.8 4.3 - - + +
589C VAL* 1.3 74.7 - - - +
591C ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 591 (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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360C ILE* 5.5 0.2 - - - +
364C TYR* 3.3 20.4 + - - -
369C PHE* 3.5 15.2 - - - -
461C ASP* 3.7 7.1 + - - -
462C ASP* 3.5 6.0 + - - +
463C ALA* 2.9 57.9 + - - +
465C ILE* 4.7 6.7 - - - -
479C CYS* 4.3 20.9 - - + -
482C PHE* 3.2 34.1 - - - -
483C LEU* 5.9 2.9 - - + -
560C THR* 3.2 17.3 - - - +
561C ILE* 4.1 14.6 - - + -
589C VAL* 4.7 2.9 - - + -
590C HIS* 1.3 77.4 - - - +
592C ALA* 1.3 76.2 - - - +
593C ILE* 4.3 12.4 - - + +
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Residues in contact with ALA 592 (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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460C GLN* 5.3 7.9 - - + +
461C ASP* 3.2 20.9 - - - +
462C ASP* 4.8 3.6 - - - +
483C LEU* 4.7 2.3 - - - +
558C CYS 4.9 2.5 - - - +
559C ALA* 3.2 6.7 - - - +
560C THR* 3.2 33.7 + - + +
591C ARG* 1.3 84.4 - - - +
593C ILE* 1.3 66.8 + - - +
595C GLY* 4.5 13.5 - - - +
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Residues in contact with ILE 593 (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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360C ILE* 5.2 2.2 - - + -
461C ASP* 3.3 11.8 + - - +
482C PHE* 3.5 50.5 - - + -
483C LEU* 3.5 29.2 - - + +
486C VAL* 4.1 21.1 - - + -
487C TYR* 2.9 48.2 + - + +
558C CYS* 3.2 12.4 - - - +
559C ALA* 4.1 1.1 - - - -
591C ARG* 4.3 9.9 - - + +
592C ALA* 1.3 79.1 - - - +
594C LEU* 1.3 66.0 + - + +
595C GLY 3.0 4.9 + - - -
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Residues in contact with LEU 594 (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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356C LEU* 4.3 22.4 - - + +
357C ILE* 5.6 0.2 - - - -
359C PHE* 5.6 0.2 - - + -
360C ILE* 3.5 35.0 - - + -
437C PHE* 5.8 0.4 - - + -
461C ASP* 3.0 23.7 + - + +
486C VAL* 4.5 3.8 - - + -
487C TYR* 5.8 0.2 - - + -
490C PHE* 3.8 25.8 - - + -
558C CYS* 4.1 12.2 - - - -
593C ILE* 1.3 77.2 - - + +
595C GLY* 1.3 62.3 + - - +
596C SER 3.1 17.1 + - - +
597C VAL* 4.4 17.7 - - + -
599C ARG* 4.7 1.4 - - - +
600C MET* 3.8 37.6 + - + +
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Residues in contact with GLY 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C GLN* 3.2 22.4 - - - +
461C ASP* 2.9 18.7 + - - +
558C CYS* 3.7 19.4 + - - -
592C ALA* 4.6 7.7 - - - +
593C ILE 3.0 7.7 + - - +
594C LEU* 1.3 77.2 - - - +
596C SER* 1.3 59.1 + - - -
599C ARG* 5.6 2.7 - - - -
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Residues in contact with SER 596 (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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455C VAL* 5.5 2.6 - - - +
458C PHE* 3.9 38.8 - - - -
459C GLN 3.6 5.6 - - - -
460C GLN* 4.3 2.5 - - - +
594C LEU* 3.1 8.5 + - - +
595C GLY* 1.3 73.0 - - - -
597C VAL* 1.3 63.8 + - - +
598C GLU* 3.9 1.8 - - - -
599C ARG* 3.7 28.7 - - - +
600C MET* 3.0 20.6 + - - +
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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