Contacts of the strand formed by residues 612 - 619 (chain A) 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 LEU 612 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A PRO* 3.8 9.0 - - + -
611A GLN* 1.3 70.3 - - - +
613A GLN* 1.3 65.1 + - - +
638A ALA 3.5 2.5 - - - +
639A ASN* 3.7 29.4 - - + -
644A ALA* 4.0 11.0 - - + -
647A ALA* 5.7 0.4 - - + -
693A MET* 4.0 18.8 - - + -
723A ILE* 3.8 30.7 - - + +
725A SER* 4.3 12.1 - - - +
730A ASN* 4.7 4.5 - - - +
731A PRO 3.1 29.4 - - - +
732A ASN 4.6 1.5 + - - -
733A SER* 3.2 32.4 - - - +
734A LYS 4.5 1.4 + - - -
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A GLN* 3.7 35.1 + - - +
612A LEU* 1.3 77.8 + - - +
614A LEU* 1.3 61.2 + - - +
615A THR* 6.1 2.5 - - + -
636A ASP 4.5 0.7 - - - -
637A ALA* 3.5 0.3 - - - -
638A ALA* 2.6 45.8 + - + +
640A GLU* 4.2 30.3 + - + +
723A ILE* 3.3 10.4 - - - +
733A SER* 4.7 0.2 - - - -
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Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 1.3 76.5 + - - +
615A THR* 1.3 74.6 - - - +
616A ALA* 5.4 0.4 - - + -
635A MET* 4.5 12.1 - - + -
636A ASP 3.6 17.5 - - - +
637A ALA* 4.0 18.2 - - + -
649A LEU* 4.3 7.9 - - + -
721A LEU* 3.7 18.2 - - + +
722A GLN* 3.7 39.0 - - - +
723A ILE* 4.0 7.4 - - + +
733A SER* 4.1 13.1 - - - +
734A LYS 4.5 2.2 - - - +
736A VAL* 3.4 27.9 - - + +
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Residues in contact with THR 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 6.1 2.2 - - + -
614A LEU* 1.3 82.6 - - - +
616A ALA* 1.3 62.3 + - - +
635A MET* 3.3 4.0 - - - +
636A ASP* 2.8 47.7 + - - +
736A VAL* 4.8 3.1 - - - -
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A LEU* 5.4 1.3 - - + -
615A THR* 1.3 77.0 - - - +
617A SER* 1.3 66.8 + - - +
633A LEU* 6.4 0.4 - - + -
634A GLN 3.3 11.4 - - - +
635A MET* 3.7 12.3 - - + -
721A LEU* 4.1 12.8 - - + -
736A VAL* 4.2 17.7 - - + +
738A LEU* 4.1 25.1 - - + +
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ALA* 1.3 78.7 - - - +
618A VAL* 1.3 69.6 + - - +
619A THR* 5.8 1.3 - - - +
633A LEU* 3.8 1.4 - - - +
634A GLN* 2.8 47.1 + - - +
738A LEU* 4.1 9.2 - - - +
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Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A SER* 1.3 77.4 - - - +
619A THR* 1.3 69.2 + - - +
620A GLY 4.3 0.3 + - - -
621A SER* 4.4 15.2 - - - -
631A LEU* 3.4 38.4 - - + -
632A GLU 3.8 7.2 - - - +
633A LEU* 4.7 11.9 - - + -
719A PHE* 5.6 2.2 - - + -
738A LEU* 3.4 29.4 - - + +
740A VAL* 3.8 25.1 - - + -
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Residues in contact with THR 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A SER* 5.6 2.0 - - - +
618A VAL* 1.3 80.6 - - - +
620A GLY* 1.3 65.8 + - - +
630A VAL 5.0 0.9 - - - +
631A LEU* 3.7 3.1 - - - +
632A GLU* 3.2 44.6 + - - +
634A GLN* 3.8 35.7 - - + +
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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