Contacts of the helix formed by residues 643 - 658 (chain C) in PDB entry 5FBN
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 643 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513C GLU* 3.6 21.5 - - - +
577C LYS* 3.9 14.6 - - - +
580C ILE* 3.7 3.8 - - - -
642C PRO* 1.3 76.7 - - - +
644C PHE* 1.3 59.4 + - - +
645C LYS* 3.5 7.1 + - - +
646C ILE* 3.1 35.9 + - + +
647C LEU* 3.0 27.5 + - - +
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Residues in contact with PHE 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C CYS* 3.5 14.9 - - - +
509C MET* 3.5 54.5 - - + -
510C GLU* 3.6 24.1 - - + +
513C GLU* 3.1 30.0 + - + +
576C SER* 4.6 3.1 - - - -
579C ASP* 3.7 30.3 - - + -
580C ILE* 3.6 23.7 - - + +
583C PHE* 3.6 28.3 - + + -
643C THR* 1.3 71.0 - - - +
645C LYS* 1.3 59.9 + - - +
647C LEU* 4.0 8.5 - - + -
648C LEU* 2.9 31.2 + - - +
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Residues in contact with LYS 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510C GLU* 3.8 32.9 + - + +
513C GLU* 3.5 7.8 + - - +
643C THR* 3.2 8.9 - - - +
644C PHE* 1.3 77.9 - - - +
646C ILE* 1.3 64.1 + - + +
648C LEU* 3.5 4.1 + - + +
649C SER* 3.1 22.8 + - - -
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Residues in contact with ILE 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C PRO* 4.0 15.5 - - + -
643C THR* 3.1 33.7 + - + +
645C LYS* 1.3 75.3 - - + +
647C LEU* 1.3 66.5 + - - +
649C SER* 3.2 8.3 + - - -
650C ASN* 2.9 40.0 + - - +
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Residues in contact with LEU 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C CYS* 3.7 14.4 - - - -
580C ILE* 3.8 22.7 - - + -
583C PHE* 3.7 26.2 - - + -
629C ILE* 3.7 23.3 - - + -
632C SER* 3.9 4.7 - - - +
633C CYS* 3.7 22.2 - - - -
642C PRO* 3.6 22.7 - - + -
643C THR 3.0 20.5 + - - +
644C PHE* 3.7 6.7 - - + +
646C ILE* 1.3 74.9 - - - +
648C LEU* 1.3 58.1 + - - +
650C ASN* 3.2 10.2 + - - +
651C ILE* 2.9 34.2 + - + +
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Residues in contact with LEU 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C LYS* 4.1 24.5 - - + +
506C CYS* 3.4 15.6 - - + +
507C GLU* 3.8 33.2 - - + -
510C GLU* 3.5 26.2 - - + +
644C PHE 2.9 17.8 + - - +
645C LYS* 3.7 5.4 - - + +
647C LEU* 1.3 76.1 - - - +
649C SER* 1.3 57.6 + - - +
651C ILE* 3.1 5.6 + - + +
652C LEU* 2.8 48.0 + - + +
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Residues in contact with SER 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C LYS* 3.1 11.1 + - - -
646C ILE* 3.5 10.5 - - - -
648C LEU* 1.3 78.8 - - - +
650C ASN* 1.3 59.9 + - - +
652C LEU* 3.5 9.1 + - - +
653C ASP* 3.1 38.2 + - - +
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Residues in contact with ASN 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C ILE* 3.7 24.2 - - + +
632C SER* 5.3 4.8 + - - -
642C PRO* 5.5 1.2 - - - +
646C ILE* 2.9 38.2 + - - +
647C LEU* 3.6 13.8 - - - +
649C SER* 1.3 76.4 + - - +
651C ILE* 1.3 64.0 + - - +
653C ASP* 3.3 12.1 + - - +
654C VAL* 3.1 27.0 + - - +
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Residues in contact with ILE 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C LEU* 3.9 22.9 - - + -
502C CYS* 4.2 10.5 - - + +
503C LYS* 3.9 28.5 - - + +
506C CYS* 4.0 17.5 - - + -
583C PHE* 4.0 30.1 - - + -
587C MET* 4.8 3.1 - - + -
629C ILE* 4.1 23.6 - - + -
647C LEU 2.9 23.3 + - - +
648C LEU* 3.6 4.7 - - - +
650C ASN* 1.3 69.1 - - - +
652C LEU* 1.3 61.6 + - - +
654C VAL* 3.2 5.6 + - - +
655C MET* 2.9 31.7 + - - +
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Residues in contact with LEU 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C LYS* 3.4 40.4 - - + -
648C LEU* 2.8 43.7 + - + +
649C SER* 3.9 7.9 - - - +
651C ILE* 1.3 72.2 - - - +
653C ASP* 1.3 64.0 + - - +
655C MET* 3.3 10.2 + - + +
656C ASP* 3.0 33.4 + - - +
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Residues in contact with ASP 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C SER* 3.1 27.0 + - - +
650C ASN* 3.3 14.4 + - - +
652C LEU* 1.3 78.5 - - - +
654C VAL* 1.3 56.3 + - + +
656C ASP* 3.3 8.9 + - - +
657C GLU* 3.0 42.4 + - - +
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Residues in contact with VAL 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C LEU* 3.6 20.2 - - + -
625C LYS* 3.9 22.9 - - + +
626C VAL* 4.0 10.3 - - + -
629C ILE* 3.8 20.2 - - + -
650C ASN 3.1 14.0 + - - +
651C ILE 3.2 7.4 + - - +
653C ASP* 1.3 72.5 - - + +
655C MET* 1.3 58.5 + - - +
657C GLU* 3.1 8.4 + - - +
658C GLU* 2.7 62.6 + - + +
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Residues in contact with MET 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C GLN* 4.9 15.4 - - + +
499C LEU* 3.4 21.1 - - + -
500C GLU* 3.8 39.5 - - + +
503C LYS* 3.7 30.5 - - + -
651C ILE* 2.9 27.8 + - - +
652C LEU* 3.3 14.6 + - + +
654C VAL* 1.3 75.7 - - - +
656C ASP* 1.3 65.1 + - - +
658C GLU 3.6 16.2 - - - +
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Residues in contact with ASP 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C LEU* 3.0 26.4 + - - +
653C ASP* 3.7 9.0 - - - +
654C VAL 3.2 0.2 - - - -
655C MET* 1.3 80.0 - - - +
657C GLU* 1.3 61.4 + - + +
658C GLU 4.9 0.6 - - - +
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Residues in contact with GLU 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C LYS* 3.7 35.5 + - - +
653C ASP* 3.0 30.6 + - - +
654C VAL* 3.7 4.6 - - - +
656C ASP* 1.3 80.6 - - + +
658C GLU* 1.3 69.9 + - + +
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Residues in contact with GLU 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C GLN* 5.8 8.9 - - - +
499C LEU* 5.8 1.8 - - + -
623C SER* 2.8 35.6 + - - -
625C LYS* 3.5 23.7 + - + +
626C VAL* 4.2 2.8 - - - +
654C VAL* 2.7 41.1 + - + +
655C MET* 3.6 15.0 - - - +
656C ASP 4.9 0.7 - - - +
657C GLU* 1.3 82.6 - - + +
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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