Contacts of the helix formed by residues 607 - 618 (chain C) in PDB entry 1XFV
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 ASN 607 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591C ASN* 3.8 11.9 - - - +
605C THR 3.7 0.2 - - - -
606C LYS* 1.3 91.3 - - - +
608C TRP* 1.3 60.7 + - - +
609C GLU* 2.8 24.6 + - + +
610C MET* 3.5 31.0 - - + +
611C THR* 2.9 28.2 + - - -
613C ARG* 5.6 3.0 - - - +
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Residues in contact with TRP 608 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495C PHE* 3.5 31.4 - + - -
588C GLU 4.8 1.8 - - - -
589C LYS* 3.5 42.6 - - + -
590C ASP 3.3 37.0 - - - +
591C ASN* 4.2 9.5 + - - +
593C ILE* 5.6 0.4 - - + -
607C ASN* 1.3 72.5 - - - +
609C GLU* 1.3 78.0 + - + +
611C THR* 3.9 6.3 - - + -
612C GLY* 3.3 14.2 + - - -
632C TYR* 3.3 26.2 - + - -
643C ILE* 3.3 24.8 - - + +
644C GLU* 2.6 28.4 + - + -
645C TRP* 3.6 26.6 - + - -
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Residues in contact with GLU 609 (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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589C LYS* 5.0 5.7 + - - -
607C ASN* 2.8 19.0 - - + +
608C TRP* 1.3 91.2 + - + +
610C MET* 1.3 68.6 + - - +
611C THR 3.0 0.9 - - - -
612C GLY* 2.6 16.9 + - - -
613C ARG* 2.8 31.5 + - - +
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Residues in contact with MET 610 (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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293C ILE* 4.1 18.8 - - + -
294C ASP* 2.9 32.5 - - + +
295C VAL* 4.0 4.7 - - + -
605C THR* 3.9 10.8 - - + -
606C LYS* 3.3 44.9 - - + -
607C ASN* 3.3 28.4 + - + +
609C GLU* 1.3 77.2 - - - +
611C THR* 1.3 52.1 + - - +
613C ARG* 2.8 25.9 + - - +
614C PHE* 2.4 38.8 + - + +
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Residues in contact with THR 611 (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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327C LEU* 5.2 1.8 - - + -
495C PHE* 4.4 18.8 - - + -
591C ASN 3.9 1.0 + - - -
593C ILE* 3.9 19.1 - - + +
595C ILE* 5.6 0.2 - - + -
605C THR* 2.6 40.5 + - + +
607C ASN 2.9 12.5 + - - -
608C TRP* 3.9 8.2 - - + -
609C GLU 2.8 3.2 + - - -
610C MET* 1.3 69.6 - - - +
612C GLY* 1.3 57.3 + - - +
613C ARG 2.8 10.2 + - - -
614C PHE* 4.2 0.9 - - - +
615C ILE* 2.9 54.3 + - + +
645C TRP* 4.5 2.5 - - + -
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Residues in contact with GLY 612 (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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608C TRP 3.3 6.5 + - - -
609C GLU 2.6 13.6 + - - -
611C THR* 1.3 76.5 - - - +
613C ARG* 1.3 56.1 + - - -
615C ILE* 4.2 2.6 - - - +
616C GLU* 3.2 29.8 + - - +
645C TRP* 3.8 31.6 - - - -
646C THR* 4.5 6.4 + - - -
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Residues in contact with ARG 613 (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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293C ILE* 3.4 33.4 - - + +
607C ASN* 5.6 2.8 - - - +
609C GLU* 2.8 22.7 + - - +
610C MET* 2.8 34.9 + - - +
612C GLY* 1.3 79.2 - - - +
614C PHE* 1.3 60.0 + - - +
615C ILE 2.8 6.1 + - - -
616C GLU* 2.9 23.7 + - - +
617C LYS* 3.0 15.3 + - - +
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Residues in contact with PHE 614 (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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293C ILE* 3.8 23.2 - - + +
295C VAL* 5.0 9.6 - - + -
325C TYR* 3.9 30.5 - + - -
595C ILE* 3.1 37.9 - - + -
603C ILE* 3.7 39.7 - - + -
605C THR* 4.5 10.5 - - + -
610C MET* 2.4 31.4 + - + +
611C THR 4.0 2.2 - - - +
613C ARG* 1.3 67.1 - - - +
615C ILE* 1.3 63.5 + - + +
617C LYS* 5.7 0.2 - - - -
618C ASN* 2.7 54.7 + - + +
619C ILE* 4.9 3.6 - - + -
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Residues in contact with ILE 615 (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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327C LEU* 4.1 15.7 - - + -
495C PHE* 4.5 1.3 - - + -
611C THR* 2.9 44.6 - - + +
612C GLY* 4.4 4.0 - - - +
613C ARG 2.8 0.8 - - - -
614C PHE* 1.3 84.9 - - + +
616C GLU* 1.3 56.7 + - - +
617C LYS 3.1 1.6 - - - -
619C ILE* 3.0 38.0 + - + +
620C THR* 2.5 44.4 + - - +
626C TYR* 4.2 22.7 - - + +
645C TRP* 3.7 20.2 - - + -
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Residues in contact with GLU 616 (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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612C GLY 3.2 20.9 + - - +
613C ARG* 2.9 16.9 + - - +
615C ILE* 1.3 77.0 - - - +
617C LYS* 1.3 60.8 + - + +
620C THR* 3.4 16.7 - - + +
621C GLY* 3.0 27.7 + - - -
646C THR* 3.5 26.4 + - - +
95Q ASP 5.5 2.6 - - - +
96Q GLY* 6.0 1.7 - - - -
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Residues in contact with LYS 617 (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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292C ARG* 2.8 55.9 - - - +
293C ILE* 3.6 20.6 - - + +
613C ARG 3.0 13.1 + - - +
614C PHE* 4.4 0.8 - - - -
616C GLU* 1.3 81.1 - - + +
618C ASN* 1.3 85.1 + - - +
621C GLY 4.7 2.4 - - - +
622C LYS* 4.4 14.6 - - - +
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Residues in contact with ASN 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.2 32.1 + - + +
614C PHE* 2.7 43.6 + - + +
616C GLU 4.8 0.2 - - - -
617C LYS* 1.3 112.8 + - - +
619C ILE* 1.3 64.4 + - - +
622C LYS* 2.8 30.1 - - - +
624C TYR* 4.0 4.9 - - - -
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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