Contacts of the helix formed by residues 606 - 613 (chain u) in PDB entry 6FF7
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 606 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604u ALA 4.1 0.8 + - - -
605u GLY* 1.3 74.1 - - - -
607u ALA* 1.3 66.5 + - - +
608u THR 3.2 2.0 - - - -
609u MET* 3.3 7.6 + - - +
610u ILE* 3.2 22.1 + - - +
639u LEU* 5.7 8.7 - - + -
643u SER* 5.6 12.3 - - - +
644u LEU* 6.2 4.5 - - + -
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Residues in contact with ALA 607 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y ILE* 3.7 27.6 - - + +
88Y ASN* 4.0 16.8 - - + +
91Y GLY* 4.4 10.8 - - - -
606u LEU* 1.3 76.4 - - - +
608u THR* 1.3 59.1 + - - +
610u ILE* 4.0 6.1 - - - +
611u SER* 2.9 31.7 + - - -
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Residues in contact with THR 608 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Y GLY* 5.3 2.4 - - - -
568u ARG* 4.9 21.8 - - - -
571u VAL* 5.3 4.7 - - - +
604u ALA* 3.8 29.8 + - - -
606u LEU 3.2 0.6 - - - +
607u ALA* 1.3 79.5 - - - +
609u MET* 1.3 56.6 + - - +
611u SER* 3.7 4.0 - - - -
612u THR* 2.9 32.7 + - - -
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Residues in contact with MET 609 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571u VAL* 6.0 2.0 - - - -
601u ALA* 5.9 4.5 - - + -
604u ALA* 5.8 2.8 - - + +
605u GLY 4.6 10.0 + - - +
606u LEU* 3.3 11.7 + - - +
608u THR* 1.3 79.6 - - - +
610u ILE* 1.3 57.2 + - - +
612u THR* 3.8 4.7 - - - -
613u MET* 2.9 35.2 + - - +
635u VAL* 5.4 11.9 - - + -
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Residues in contact with ILE 610 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606u LEU 3.2 15.1 + - - +
607u ALA* 4.0 6.5 - - - +
608u THR 3.4 0.2 - - - -
609u MET* 1.3 77.1 - - - +
611u SER* 1.3 62.0 + - - +
612u THR 3.4 0.3 + - - -
613u MET* 4.2 0.8 - - - -
614u ARG* 3.3 26.2 + - - +
644u LEU* 6.3 2.0 - - + -
647u PHE* 5.6 10.8 - - + -
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Residues in contact with SER 611 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y GLY 3.5 29.4 - - - -
92Y PHE* 4.0 11.0 - - - -
607u ALA 2.9 19.8 + - - -
608u THR* 4.1 4.0 - - - -
610u ILE* 1.3 76.4 - - - +
612u THR* 1.3 59.8 + - - +
614u ARG* 4.4 7.8 + - - +
615u PRO 5.4 0.5 - - - -
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Residues in contact with THR 612 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571u VAL* 4.3 22.7 - - - -
572u HIS* 4.9 17.1 - - - +
608u THR 2.9 19.4 + - - -
609u MET* 3.8 5.2 - - - -
610u ILE 3.2 0.2 - - - -
611u SER* 1.3 77.4 - - - +
613u MET* 1.3 58.4 + - - +
614u ARG 3.2 8.2 + - - -
615u PRO* 4.2 7.6 - - - +
616u ASP* 5.0 1.7 + - - +
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Residues in contact with MET 613 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609u MET 2.9 19.3 + - - +
610u ILE* 4.2 1.3 - - - -
612u THR* 1.3 71.7 - - - +
614u ARG* 1.3 61.9 + - - +
615u PRO 3.7 0.7 - - - -
616u ASP* 3.7 23.3 + - + +
617u ILE* 4.4 2.9 + - - +
628u THR* 5.2 13.9 - - - +
631u ALA* 6.1 3.8 - - + -
632u PHE* 6.6 0.2 - - + -
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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