Contacts of the strand formed by residues 484 - 489 (chain A) in PDB entry 6F3T
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 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A VAL* 3.6 5.2 - - - +
479A THR* 3.1 36.8 + - + -
482A SER 3.6 0.2 - - - -
483A SER* 1.3 92.3 - - - +
485A ILE* 1.3 65.7 + - - +
496A VAL* 4.3 15.0 - - + -
497A TRP 3.3 7.0 - - - +
498A SER* 3.9 20.9 - - - -
499A VAL* 4.1 0.2 - - - -
503A LYS 4.9 1.3 - - - +
504A LEU* 4.2 22.7 - - + +
551A PHE* 3.7 30.2 - - + -
555A ARG* 4.9 9.4 - - + +
572A LEU* 4.1 17.9 - - + -
575A PHE* 5.8 1.3 - - + -
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Residues in contact with ILE 485 (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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464A TYR* 3.9 37.5 - - + +
466A PHE* 3.9 26.6 - - + -
476A VAL* 4.2 5.4 - - + -
477A ASP 3.5 11.2 - - - +
478A VAL* 4.1 14.1 - - + -
484A LEU* 1.3 78.6 - - - +
486A ALA* 1.3 68.3 + - - +
495A ARG 3.6 1.0 - - - +
496A VAL* 3.3 2.6 - - - +
497A TRP* 2.8 52.3 + - + +
499A VAL* 3.7 20.2 - - + -
551A PHE* 4.1 2.5 - - - -
792A LEU* 4.7 12.8 - - + -
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A PHE* 4.2 2.9 - - - -
476A VAL* 3.3 9.4 - - - +
477A ASP 3.0 33.2 + - - +
485A ILE* 1.3 73.2 - - - +
487A GLY* 1.3 60.2 + - - +
488A GLY 4.3 0.2 - - - -
494A VAL* 4.8 3.8 - - + -
495A ARG 3.3 6.7 - - - +
496A VAL* 4.4 2.7 - - + -
549A ALA* 4.8 5.6 - - + +
551A PHE* 3.5 25.7 - - + -
558A LEU* 3.9 27.4 - - + -
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Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A PHE* 3.6 19.6 - - - -
473A LEU* 4.2 2.0 - - - -
475A ALA 3.3 7.6 - - - -
476A VAL* 4.7 0.7 - - - -
486A ALA* 1.3 76.1 - - - +
488A GLY* 1.3 60.3 + - - -
489A PHE* 3.3 13.2 - - - -
494A VAL* 3.4 7.0 - - - -
495A ARG 2.9 35.4 + - - -
549A ALA* 5.6 0.7 - - - -
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 3.6 2.6 - - - +
474A THR* 2.8 29.8 + - - -
475A ALA* 2.8 16.3 + - - +
487A GLY* 1.3 73.9 - - - -
489A PHE* 1.3 63.6 + - - -
493A THR 3.7 6.1 - - - -
494A VAL* 4.6 2.4 - - - +
546A VAL* 3.7 25.4 - - - -
549A ALA* 5.2 2.6 - - - +
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Residues in contact with PHE 489 (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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466A PHE* 3.8 17.3 - + - -
467A LEU* 4.0 9.4 - - + -
470A TYR* 3.5 42.4 - + + -
471A GLN 4.7 0.7 - - - +
472A GLY 3.2 6.7 - - - +
473A LEU* 3.6 39.7 - - + -
474A THR* 3.4 6.5 + - - -
487A GLY* 3.3 26.2 - - - -
488A GLY* 1.3 71.4 - - - -
490A ALA* 1.3 60.7 + - - +
491A ASP* 3.2 21.8 - - - +
492A SER* 2.9 16.8 + - - -
493A THR* 3.2 12.9 + - - +
495A ARG* 3.6 27.1 - - + -
546A VAL* 3.1 16.4 + - - +
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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