Contacts of the strand formed by residues 565 - 572 (chain C) in PDB entry 3FCS
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 ILE 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466C LEU* 4.2 17.3 - - + -
485C PHE* 5.9 0.2 - - + -
511C ASP* 3.4 29.2 - - + +
520C ARG* 3.4 25.8 - - + +
521C VAL* 3.7 39.9 - - + -
552C LEU* 4.2 10.3 - - + -
563C SER 4.4 2.0 - - - +
564C PRO* 1.3 69.7 - - - +
566C VAL* 1.3 60.8 + - - +
567C LEU* 3.7 7.7 + - + +
595C GLN* 3.4 2.6 - - - -
596C THR* 2.6 47.2 + - + +
597C ARG* 4.7 3.4 - - - -
598C ILE* 4.5 15.0 - - + -
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Residues in contact with VAL 566 (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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509C GLN 3.7 0.9 - - - +
510C LEU 3.7 0.2 - - - -
511C ASP* 2.8 31.0 + - - +
512C ARG* 2.9 20.5 + - + +
513C GLN* 3.6 34.5 - - + +
564C PRO* 3.6 12.5 + - + +
565C ILE* 1.3 74.1 - - - +
567C LEU* 1.3 64.9 + - - +
593C GLN* 3.7 30.7 - - + +
594C GLU 3.7 9.9 - - - +
595C GLN* 4.2 18.4 - - - +
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Residues in contact with LEU 567 (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 LEU* 3.1 18.7 - - + +
462C VAL* 3.6 40.6 - - + -
485C PHE* 4.8 3.6 - - + -
487C ILE* 3.9 24.2 - - + -
508C LEU* 4.9 3.8 - - + -
509C GLN 3.5 2.9 - - - +
510C LEU* 3.8 31.0 - - + -
511C ASP 4.0 2.7 - - - +
521C VAL* 4.8 2.7 - - + -
565C ILE* 4.1 16.4 - - + +
566C VAL* 1.3 81.5 - - - +
568C SER* 1.3 60.7 + - - +
593C GLN* 3.3 2.6 - - - +
594C GLU* 2.8 40.2 + - + +
595C GLN* 5.1 0.2 - - - -
596C THR* 5.0 4.0 - - + -
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Residues in contact with SER 568 (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 LEU* 3.9 2.9 - - - -
507C GLU 3.5 1.0 + - - +
508C LEU* 3.4 7.8 - - - +
509C GLN* 3.0 39.9 + - - +
512C ARG* 3.3 40.4 + - - -
566C VAL 4.2 0.4 + - - -
567C LEU* 1.3 74.6 - - - +
569C LEU* 1.3 61.0 + - - +
570C ASN* 5.2 1.4 + - - +
591C HIS* 4.0 8.2 - - - -
592C VAL 3.5 3.6 - - - -
593C GLN* 3.8 17.5 - - - -
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Residues in contact with LEU 569 (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 VAL* 4.6 4.0 - - + +
459C GLN 3.7 30.1 - - - +
460C LEU* 4.0 10.9 - - + +
489C MET* 3.5 43.5 - - + -
491C VAL* 4.0 19.3 - - + -
506C ALA* 3.9 13.2 - - + -
507C GLU 3.4 11.9 - - - +
508C LEU* 4.4 3.6 - - + +
568C SER* 1.3 75.3 - - - +
570C ASN* 1.3 64.9 + - - +
571C VAL* 4.7 6.7 - - + -
590C THR 3.7 1.4 - - - +
591C HIS* 3.4 6.1 + - - -
592C VAL* 3.0 41.1 + - + +
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Residues in contact with ASN 570 (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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506C ALA* 3.5 0.9 - - - -
507C GLU* 2.8 45.4 + - + +
512C ARG* 6.0 2.7 - - - +
568C SER* 5.5 2.0 - - - +
569C LEU* 1.3 74.6 - - - +
571C VAL* 1.3 70.2 + - - +
572C SER* 5.4 0.2 - - - -
590C THR* 3.6 6.2 + - - +
591C HIS* 3.7 22.9 + - + +
3570C NAG 1.4 71.9 + - - +
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Residues in contact with VAL 571 (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 ALA* 4.8 5.8 - - + -
458C VAL* 3.5 27.4 - - + -
491C VAL* 3.7 25.8 - - + -
504C LEU* 3.4 36.1 - - + -
505C ASN 3.2 7.4 - - - +
506C ALA* 4.2 9.2 - - + -
569C LEU* 4.7 2.9 - - + -
570C ASN* 1.3 81.1 + - - +
572C SER* 1.3 67.0 + - - +
586C LEU* 4.3 6.4 - - + +
590C THR* 2.8 32.1 + - - +
3570C NAG 4.1 0.4 - - - -
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Residues in contact with SER 572 (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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504C LEU* 3.3 12.2 - - - +
505C ASN* 2.8 42.7 + - - +
571C VAL* 1.3 75.9 - - - +
573C LEU* 1.3 67.7 + - - +
586C LEU* 4.0 7.0 - - - -
3570C NAG 2.8 31.6 + - - -
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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