Contacts of the strand formed by residues 493 - 497 (chain F) in PDB entry 6T8B
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 ARG 493 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489F PRO* 2.9 34.8 + - - +
492F ALA* 1.3 77.2 + - - +
494F LEU* 1.3 62.9 + - - +
511F PRO 3.8 10.9 + - - -
512F HIS* 3.1 20.9 - - - +
513F LEU 3.3 14.6 + - - -
514F LEU* 3.4 40.6 - - + +
588F PRO* 3.9 23.5 - - + +
589F THR 3.6 5.1 + - - -
590F ILE* 3.3 15.1 - - + +
591F VAL 3.2 19.6 + - - -
715F ASP* 4.2 20.3 + - - -
717F ILE* 5.5 1.6 - - - +
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Residues in contact with LEU 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480F LEU* 4.1 27.1 - - + -
483F ILE* 4.1 23.1 - - + -
484F LEU* 4.8 8.7 - - + -
493F ARG* 1.3 72.9 - - - +
495F ILE* 1.3 68.8 + - - +
496F MET* 4.5 13.2 - - + -
507F TYR* 6.0 1.8 - - + -
510F ILE* 4.0 24.5 - - + -
512F HIS* 2.4 31.8 + - + +
513F LEU* 3.5 12.5 - - + -
514F LEU* 3.3 22.2 + - - +
591F VAL* 3.6 34.8 - - + +
593F VAL* 5.0 0.7 - - + -
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Residues in contact with ILE 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F LEU* 1.3 80.9 - - - +
496F MET* 1.3 60.7 + - - +
497F ILE* 5.4 4.5 - - + -
513F LEU* 5.1 1.1 - - - -
514F LEU* 3.7 19.5 - - + +
515F CYS* 4.8 11.0 - - + +
518F VAL* 5.7 0.9 - - + -
527F ALA* 4.7 20.9 - - + +
528F LEU* 5.7 0.9 - - + -
530F TRP* 3.6 33.0 - - + -
531F SER* 3.9 13.5 - - - +
590F ILE* 3.7 22.4 - - + -
591F VAL 3.1 9.8 + - - +
592F VAL* 3.3 17.3 - - + +
593F VAL 2.8 32.2 + - - +
720F ILE* 5.2 1.3 - - + -
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Residues in contact with MET 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480F LEU* 3.8 12.6 - - + -
494F LEU* 4.5 12.6 - - + -
495F ILE* 1.3 81.5 - - - +
497F ILE* 1.3 64.4 + - - +
504F LEU* 3.6 45.8 - - + +
507F TYR* 3.6 31.0 - - + -
513F LEU* 3.7 28.7 - - + +
515F CYS* 5.8 2.0 - - - +
516F PRO 4.1 2.6 + - - +
517F VAL* 5.4 11.4 - - + -
518F VAL* 3.3 30.6 + - - +
593F VAL* 3.6 17.0 - - + +
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Residues in contact with ILE 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ILE* 5.4 6.5 - - + -
496F MET* 1.3 76.4 - - - +
498F ASP* 1.3 67.5 + - - +
499F PRO* 3.9 14.4 - - + -
504F LEU* 3.7 8.7 - - - +
518F VAL* 3.8 22.0 - - + +
521F MET* 4.0 9.4 - - + -
524F ALA* 4.1 12.3 - - + +
527F ALA* 5.4 2.7 - - + -
528F LEU* 3.7 26.2 - - + -
592F VAL* 5.0 1.8 - - + -
593F VAL 2.9 14.7 + - - +
594F VAL* 3.7 16.6 - - + -
595F ASP 3.5 18.4 + - - -
600F MET* 3.7 36.3 - - + -
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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