Contacts of the strand formed by residues 606 - 613 (chain C) in PDB entry 5NC5
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 606 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C PHE* 5.1 1.6 - - + -
598C TYR* 3.7 26.0 - - + +
599C LEU* 5.0 6.3 - - + +
602C GLU* 3.0 30.1 + - + +
603C LYS* 3.6 8.0 - - - +
605C ASN* 1.3 77.0 - - + +
607C GLU* 1.3 63.3 + - - +
608C SER* 3.7 22.7 - - - +
609C VAL* 3.9 15.3 - - + -
629C VAL* 3.8 23.1 - - + -
630C SER 3.9 3.4 - - - -
631C LEU* 3.9 11.0 - - + -
632C LYS* 3.6 12.9 + - - -
647C ILE* 5.2 1.3 - - + -
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Residues in contact with GLU 607 (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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282C ASN* 4.0 9.0 + - - +
599C LEU* 5.5 2.4 - - - +
605C ASN 3.6 3.0 + - - -
606C VAL* 1.3 75.1 - - - +
608C SER* 1.3 68.8 + - - +
630C SER* 3.0 11.9 + - - +
631C LEU 3.8 20.9 - - - +
632C LYS* 3.7 26.1 - - + +
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Residues in contact with SER 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 3.6 24.6 - - - -
282C ASN* 3.2 10.5 - - - -
325C TYR 4.9 0.7 + - - -
326C PRO* 3.7 27.7 + - - +
599C LEU* 5.6 0.2 - - - -
606C VAL* 3.7 2.1 - - - +
607C GLU* 1.3 88.2 - - - +
609C VAL* 1.3 68.3 + - - +
628C PHE 3.9 0.4 - - - +
629C VAL* 3.6 4.0 - - - +
630C SER* 3.1 33.7 + - - +
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Residues in contact with VAL 609 (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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280C GLU 3.8 1.2 - - - +
281C PHE* 3.6 6.4 - - - -
282C ASN* 2.9 33.5 + - - +
595C THR* 4.1 29.4 - - + +
598C TYR* 3.8 33.7 - - + -
599C LEU* 4.3 15.0 - - + -
606C VAL* 3.9 7.4 - - + -
608C SER* 1.3 81.0 - - - +
610C PHE* 1.4 64.2 + - - +
611C ALA* 3.9 2.7 + - + +
627C ALA* 4.2 22.7 - - + -
628C PHE 3.5 6.3 - - - +
629C VAL* 4.7 3.6 - - + -
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Residues in contact with PHE 610 (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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139C VAL* 4.1 11.4 - - + -
141C GLY* 4.0 12.3 - - - -
178C PHE* 3.7 23.1 - + - -
279C ALA* 3.9 16.6 - - + -
280C GLU 3.5 5.4 - - - -
281C PHE* 4.0 14.4 - + + -
286C ALA* 4.2 12.8 - - + -
287C SER 3.5 28.9 - - - -
288C GLY* 4.2 5.6 - - - -
324C VAL* 5.3 0.2 - - + -
326C PRO* 3.6 33.1 - - + +
609C VAL* 1.4 69.7 - - - +
611C ALA* 1.3 59.6 + - - +
612C VAL* 3.9 15.9 - - + -
627C ALA* 3.6 0.7 - - - -
628C PHE* 2.8 56.2 + + + +
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Residues in contact with ALA 611 (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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278C ILE 3.8 1.2 - - - +
279C ALA* 3.4 2.8 - - - +
280C GLU* 2.9 43.6 + - + +
588C GLN* 5.7 3.1 - - - +
591C LEU* 4.1 22.7 - - + -
595C THR* 3.9 21.3 - - + +
609C VAL* 3.8 7.1 - - + +
610C PHE* 1.3 72.4 - - - +
612C VAL* 1.3 61.5 + - - +
613C ASN 4.1 0.7 - - - -
626C ILE 3.6 4.0 - - - -
627C ALA* 4.2 3.6 - - + +
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Residues in contact with VAL 612 (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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178C PHE* 3.9 28.9 - - + -
277C ILE* 4.5 8.5 - - + -
278C ILE 3.7 2.7 - - - -
279C ALA* 4.3 3.8 - - + -
591C LEU* 3.6 4.0 - - - +
610C PHE* 3.9 27.1 - - + -
611C ALA* 1.3 77.0 - - - +
613C ASN* 1.3 62.4 + - - +
615C PHE* 3.5 36.6 - - + +
625C GLY* 3.2 5.0 - - - -
626C ILE* 2.8 43.0 + - + +
628C PHE* 4.5 5.6 - - + -
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Residues in contact with ASN 613 (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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276C ASP 3.4 1.9 - - - +
277C ILE* 3.3 4.7 - - - -
278C ILE* 2.7 48.7 + - + +
584C GLN* 3.1 44.6 + - - +
587C THR* 3.8 12.4 - - - +
588C GLN* 3.4 34.8 + - - +
591C LEU* 3.5 16.5 - - + +
611C ALA 4.1 0.4 - - - -
612C VAL* 1.3 73.2 - - - +
614C GLY* 1.3 67.2 + - - +
615C PHE 3.6 0.4 - - - -
622C GLN* 4.0 5.0 - - - +
624C THR 3.8 0.3 - - - +
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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