Contacts of the strand formed by residues 664 - 669 (chain A) in PDB entry 3FBY
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 664 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A LYS* 3.5 42.4 - - + -
639A ALA 3.3 10.5 - - - +
640A VAL* 3.8 21.3 - - + -
641A LYS 5.1 0.2 - - - +
650A LEU* 4.4 4.3 - - + -
653A ALA* 4.0 29.6 - - + +
654A LEU* 4.4 4.7 - - + +
658A GLY 4.2 3.1 - - - +
659A ASP* 3.1 4.6 - - - +
660A THR* 2.6 35.6 + - - +
663A GLN* 1.3 87.8 - - + +
665A ARG* 1.3 68.1 + - - +
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Residues in contact with ARG 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LYS* 3.3 1.7 - - - -
639A ALA* 2.8 46.4 + - - +
659A ASP* 3.3 21.3 - - + +
664A VAL* 1.3 79.9 - - - +
666A LEU* 1.3 61.1 + - - +
667A LEU* 3.1 18.5 + - + +
714A ASP* 2.9 24.2 + - - -
716A THR* 2.6 32.7 + - - +
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLN* 3.8 19.5 - - + -
637A LEU 3.2 9.2 - - - +
638A LYS* 4.0 10.1 - - + -
657A THR* 4.1 16.4 - - + -
658A GLY* 3.9 27.2 + - - +
659A ASP* 2.6 19.4 + - - +
665A ARG* 1.3 70.2 - - - +
667A LEU* 1.3 65.2 + - - +
668A TRP* 3.1 29.1 - - - +
669A LYS* 4.1 20.4 - - + -
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Residues in contact with LEU 667 (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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610A TYR* 4.0 17.5 - - + -
637A LEU* 2.9 35.7 + - + +
639A ALA* 3.8 19.7 - - + +
665A ARG* 3.1 24.1 + - + +
666A LEU* 1.3 73.2 - - - +
668A TRP* 1.3 61.2 + - - +
695A ILE* 4.3 1.3 - - + -
712A VAL* 4.0 14.0 - - + +
714A ASP* 3.2 45.3 - - + +
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Residues in contact with TRP 668 (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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635A ILE* 3.9 24.5 - - + -
636A GLN* 3.4 0.4 - - - -
637A LEU* 2.7 51.4 + - + -
666A LEU* 3.1 12.9 - - - +
667A LEU* 1.3 80.5 - - - +
669A LYS* 1.3 81.9 + - - +
670A ASP* 3.6 27.8 - - + -
671A PRO* 4.5 8.1 - - + +
697A VAL* 4.0 18.2 - - + -
699A PHE* 4.8 1.1 - + - -
707A ALA* 4.0 16.8 - - + -
708A ASP 3.7 21.4 + - - -
709A SER* 3.4 38.7 + - - +
712A VAL* 4.2 15.3 - - + -
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Residues in contact with LYS 669 (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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632A GLU* 3.2 22.0 - - - +
633A PRO 4.7 2.0 - - - -
634A GLY 4.5 4.5 - - - +
635A ILE 3.3 11.9 - - - +
636A GLN* 4.7 1.8 - - + -
657A THR* 3.8 20.9 - - + -
666A LEU* 4.1 15.9 - - + -
668A TRP* 1.3 96.6 + - - +
670A ASP* 1.3 75.5 + - - +
671A PRO* 3.4 12.0 + - - +
673A ASN* 3.0 34.0 + - - +
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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