Contacts of the strand formed by residues 590 - 594 (chain E) 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 ILE 590 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E ARG* 3.1 22.0 - - + +
494E LEU 4.7 0.2 - - - +
495E ILE* 4.4 15.0 - - + -
514E LEU* 3.7 32.3 - - + -
530E TRP* 3.9 15.9 - - + -
534E GLU* 4.5 2.7 - - + -
538E ARG* 3.4 23.5 - - - +
588E PRO* 3.6 9.4 + - + +
589E THR* 1.3 77.5 - - - +
591E VAL* 1.3 66.0 + - - +
592E VAL* 3.6 5.8 + - + -
623E GLY 2.9 12.3 + - - +
624E ILE* 3.1 22.7 - - + +
625E HIS 2.9 20.6 + - - -
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Residues in contact with VAL 591 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439E VAL* 3.7 20.6 - - + -
456E LEU* 3.6 23.8 - - + -
480E LEU* 5.8 0.2 - - + -
483E ILE* 4.8 7.4 - - + -
492E ALA* 5.7 0.2 - - + -
493E ARG 2.6 11.7 + - - +
494E LEU* 3.3 37.2 - - + +
495E ILE 4.4 1.6 - - - -
589E THR* 5.1 1.8 - - - +
590E ILE* 1.3 74.5 - - - +
592E VAL* 1.3 57.0 + - - +
593E VAL* 3.0 11.4 + - + +
625E HIS* 3.2 17.3 - - + +
627E ILE* 3.5 37.7 - - + -
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Residues in contact with VAL 592 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ILE* 3.5 28.3 - - + +
497E ILE* 4.1 13.2 - - + -
527E ALA* 5.9 1.8 - - + +
528E LEU* 4.8 10.3 - - + -
531E SER* 4.3 23.1 - - - -
590E ILE* 3.6 12.5 + - + -
591E VAL* 1.3 68.3 - - - +
593E VAL* 1.3 57.8 + - - +
594E VAL* 3.1 27.3 + - + +
615E ILE* 5.9 0.9 - - + -
624E ILE* 4.4 13.9 - - + -
625E HIS 2.5 13.1 + - - +
626E LEU* 3.4 29.5 - - + -
627E ILE 3.5 1.0 + - - -
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Residues in contact with VAL 593 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E VAL* 5.0 5.4 - - + -
480E LEU* 3.6 36.1 - - + -
494E LEU* 3.7 16.6 - - + -
495E ILE 2.9 8.1 + - - +
496E MET* 3.5 21.0 - - + -
497E ILE* 2.8 31.0 + - - +
504E LEU* 3.6 25.4 - - + -
591E VAL* 3.4 17.3 - - + +
592E VAL* 1.3 67.8 - - - +
594E VAL* 1.3 63.5 + - - +
595E ASP* 5.2 0.7 - - + -
627E ILE* 4.5 11.0 - - + -
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Residues in contact with VAL 594 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476E VAL* 5.8 1.2 - - - +
497E ILE* 4.2 12.8 - - + -
528E LEU* 5.4 2.5 - - + -
592E VAL* 3.1 31.5 + - + +
593E VAL* 1.3 74.1 - - - +
595E ASP* 1.3 62.7 + - - +
597E PHE* 3.5 30.5 - - + -
600E MET* 3.8 15.3 - - + -
612E ILE* 5.5 0.2 - - + -
626E LEU* 3.9 10.1 - - + -
627E ILE* 2.9 27.6 - - - +
628E LEU* 3.5 32.5 - - + +
629E ALA* 3.2 6.8 + - - +
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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
------------------------------------------------------------
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