Contacts of the strand formed by residues 624 - 630 (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 ILE 624 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461F HIS* 3.8 0.4 - - - -
495F ILE* 5.2 0.2 - - + -
530F TRP* 6.0 1.3 - - + -
531F SER* 3.8 37.5 - - - +
534F GLU* 6.0 2.7 - - + -
535F MET* 4.3 18.8 - - + -
538F ARG* 5.3 2.0 - - - +
590F ILE* 3.2 37.2 - - + +
592F VAL* 4.0 8.7 - - + -
615F ILE* 5.1 9.2 - - + -
619F ALA* 3.0 47.6 - - + +
622F ALA* 3.3 11.2 + - + +
623F GLY* 1.3 76.9 - - - +
625F HIS* 1.3 70.9 + - - +
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Residues in contact with HIS 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456F LEU* 3.3 42.2 + - + +
457F ALA* 3.8 18.7 + - + -
460F PRO* 3.1 28.8 - - + +
461F HIS* 3.7 6.3 - + - -
589F THR* 3.8 13.8 - - + +
590F ILE 2.8 11.1 + - - +
591F VAL* 3.6 4.4 - - + -
592F VAL* 2.9 28.2 + - - +
615F ILE* 6.0 1.1 - - - -
619F ALA 5.1 1.1 - - - -
620F ARG 4.6 10.1 + - - -
623F GLY* 2.8 41.9 + - - -
624F ILE* 1.3 78.2 - - - +
626F LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 626 (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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461F HIS* 3.1 22.2 + - + +
462F LEU 3.0 24.6 + - - -
528F LEU* 5.8 1.1 - - + -
592F VAL* 3.3 36.6 - - + +
594F VAL* 5.3 0.9 - - + -
612F ILE* 3.8 24.9 - - + +
615F ILE* 4.7 21.5 - - + -
616F ALA* 4.9 5.2 - - + -
625F HIS* 1.3 78.3 - - - +
627F ILE* 1.3 69.2 + - - +
628F LEU* 3.8 40.2 - - + -
646F ILE* 4.8 7.9 - - + -
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Residues in contact with ILE 627 (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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441F LEU* 4.8 2.2 - - + -
456F LEU* 3.7 26.9 - - + -
459F MET* 4.4 1.1 - - + -
462F LEU* 3.7 36.6 - - + -
464F VAL* 5.3 3.8 - - + -
476F VAL* 5.6 8.3 - - + -
479F MET* 4.6 12.1 - - + -
591F VAL* 4.0 11.7 - - + -
592F VAL 2.9 8.7 + - - +
593F VAL* 3.5 28.1 - - + +
594F VAL* 3.0 25.9 + - - +
626F LEU* 1.3 83.8 - - - +
628F LEU* 1.3 61.0 + - - +
629F ALA* 3.4 12.3 + - + +
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Residues in contact with LEU 628 (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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462F LEU 2.9 11.4 + - - +
463F LEU* 3.4 27.6 - - + +
464F VAL 3.4 10.0 + - - -
594F VAL* 3.9 24.0 - - + -
597F PHE* 3.9 29.8 - - + -
612F ILE* 3.7 28.0 - - + -
626F LEU* 3.8 28.7 - - + -
627F ILE* 1.3 69.9 - - - +
629F ALA* 1.3 63.7 + - - +
630F THR* 3.7 1.7 + - - +
642F ILE* 4.0 15.7 - - + -
646F ILE* 3.8 19.7 - - + -
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Residues in contact with ALA 629 (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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464F VAL* 3.4 17.3 - - + +
472F LYS* 3.4 13.2 - - - +
476F VAL* 4.2 20.2 - - + -
594F VAL 3.1 15.0 + - - +
595F ASP* 2.9 24.0 - - - +
597F PHE* 2.7 29.5 + - - +
627F ILE* 3.4 6.4 + - + +
628F LEU* 1.3 73.7 - - - +
630F THR* 1.3 52.0 + - - +
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Residues in contact with THR 630 (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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463F LEU* 5.1 4.5 - - + -
464F VAL 2.8 23.8 + - - +
465F ALA* 3.3 27.9 - - + -
472F LYS* 3.3 14.0 - - - +
596F GLU* 4.5 0.4 - - - +
597F PHE* 3.7 20.4 - - + +
598F ALA 3.6 5.5 + - - -
628F LEU 4.6 4.7 - - - +
629F ALA* 1.3 75.2 - - - +
631F GLN* 1.3 65.5 + - - +
632F ARG 3.4 15.6 + - - +
637F VAL* 3.4 14.2 - - - +
638F ILE* 3.8 24.5 - - + -
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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