Contacts of the strand formed by residues 589 - 594 (chain F) in PDB entry 6T8G
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 THR 589 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438F THR* 4.3 10.9 + - - -
439F VAL* 3.9 28.8 - - + +
456F LEU* 5.1 0.2 - - + -
491F GLU 2.9 14.8 + - - -
492F ALA* 3.2 10.1 - - - +
493F ARG 3.0 25.8 + - - +
550F LEU* 4.4 12.0 - - - +
587F LEU 3.8 1.2 + - - -
588F PRO* 1.3 71.4 - - - +
590F ILE* 1.3 62.6 + - - +
591F VAL* 4.2 5.0 + - + +
623F GLY* 3.3 21.1 - - - +
625F HIS* 3.8 16.2 - - + +
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Residues in contact with ILE 590 (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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493F ARG* 3.6 9.6 - - + +
495F ILE* 3.9 23.8 - - + -
514F LEU* 3.8 24.5 - - + -
530F TRP* 5.2 2.5 - - + -
534F GLU* 5.8 4.3 - - + -
538F ARG* 4.0 20.4 - - - +
588F PRO* 3.5 32.3 - - + +
589F THR* 1.3 76.9 - - - +
591F VAL* 1.3 67.2 + - - +
623F GLY 3.1 8.4 + - - +
624F ILE* 3.2 33.6 - - + -
625F HIS* 2.8 26.8 + - - -
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Residues in contact with VAL 591 (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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439F VAL* 5.3 6.5 - - + -
456F LEU* 4.3 25.8 - - + -
480F LEU* 5.8 0.7 - - + -
483F ILE* 5.3 10.8 - - + -
492F ALA* 5.9 2.2 - - + -
493F ARG 3.5 6.1 + - - +
494F LEU* 3.7 20.2 - - + +
495F ILE* 2.8 33.6 + - - +
589F THR* 4.8 9.4 - - + +
590F ILE* 1.3 81.0 - - - +
592F VAL* 1.3 61.4 + - - +
593F VAL* 3.7 23.6 - - + -
625F HIS* 3.6 5.8 - - + +
627F ILE* 4.0 16.6 - - + -
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Residues in contact with VAL 592 (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* 3.4 37.2 - - + +
497F ILE* 4.5 13.2 - - + -
528F LEU* 4.5 13.2 - - + -
531F SER* 4.0 13.5 - - - +
591F VAL* 1.3 73.7 - - - +
593F VAL* 1.3 68.5 + - - +
594F VAL* 4.9 2.5 - - + -
615F ILE* 5.9 2.2 - - + -
624F ILE* 4.0 17.0 - - + -
625F HIS 2.9 9.0 + - - +
626F LEU* 3.3 27.2 - - + +
627F ILE* 2.9 24.8 + - - +
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Residues in contact with VAL 593 (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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476F VAL* 5.5 6.7 - - + -
480F LEU* 4.6 18.2 - - + -
494F LEU* 4.7 2.7 - - + -
495F ILE 3.0 14.1 + - - +
496F MET* 3.7 24.0 - - + -
497F ILE* 3.2 27.8 + - - +
504F LEU* 4.5 14.8 - - + -
591F VAL* 3.7 21.5 - - + -
592F VAL* 1.3 76.9 - - - +
594F VAL* 1.3 68.1 + - - +
627F ILE* 3.5 23.1 - - + +
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Residues in contact with VAL 594 (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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497F ILE* 3.9 15.3 - - + +
499F PRO* 4.8 3.6 - - + -
504F LEU* 5.5 0.4 - - - -
528F LEU* 6.3 1.1 - - + -
592F VAL* 4.9 6.3 - - + -
593F VAL* 1.3 81.1 - - - +
595F ASP* 1.3 65.5 + - - +
596F GLU 3.7 7.2 - - - +
597F PHE* 3.7 32.3 - - + +
600F MET* 4.1 28.5 - - + -
612F ILE* 5.4 3.1 - - + -
626F LEU* 5.3 1.1 - - + -
627F ILE 3.0 7.1 + - - +
628F LEU* 3.9 26.5 - - + -
629F ALA* 3.1 23.6 + - - +
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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