Contacts of the helix formed by residues 630 - 637 (chain G) in PDB entry 1XV9
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 HIS 630 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C VAL* 5.1 5.5 - - + +
302C ARG* 2.9 56.2 + - + +
453C GLU* 3.7 41.3 + - + +
454C MET* 4.2 11.7 - - - +
456C GLU* 4.5 4.4 + - - -
628G GLU 4.9 1.1 - - - +
629G ARG* 1.3 99.1 + - - +
631G LYS* 1.3 61.0 + - - +
632G ILE 3.8 0.9 - - - -
633G LEU* 4.2 14.8 - - + -
634G HIS* 3.3 40.4 + - - +
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Residues in contact with LYS 631 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C GLU* 3.7 6.3 + - - +
628G GLU 5.2 7.6 - - - +
629G ARG 3.0 10.9 + - - +
630G HIS* 1.3 71.5 - - - +
632G ILE* 1.3 68.7 + - + +
634G HIS* 3.6 5.7 + - - +
635G ARG* 3.5 18.9 + - - +
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Residues in contact with ILE 632 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 4.6 5.2 - - + -
449C THR* 4.1 27.4 - - + +
450C PHE* 3.2 32.3 - - + +
453C GLU* 3.1 19.1 + - - +
631G LYS* 1.3 77.6 - - + +
633G LEU* 1.3 64.8 + - - +
635G ARG* 3.4 40.8 + - - +
636G LEU* 3.0 27.0 + - + +
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Residues in contact with LEU 633 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C VAL* 4.8 10.1 - - + -
298C VAL* 4.1 34.8 - - + +
301C LEU* 3.5 37.0 - - + -
302C ARG* 4.6 1.8 - - + -
450C PHE* 4.1 21.0 - - + -
453C GLU* 3.2 17.5 + - - +
454C MET* 4.5 19.1 - - - -
630G HIS* 4.2 14.1 - - + -
631G LYS 3.4 0.4 - - - -
632G ILE* 1.3 77.1 - - - +
634G HIS* 1.3 61.1 + - - +
636G LEU* 3.6 2.3 + - + +
637G LEU* 3.3 24.6 + - + +
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Residues in contact with HIS 634 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 4.9 10.5 - - + +
295C ASP* 4.8 11.5 + - - -
298C VAL* 3.3 37.4 - - + +
628G GLU* 4.4 32.4 + - - -
629G ARG 5.7 0.2 - - - -
630G HIS* 3.3 29.2 + - + +
631G LYS* 3.6 6.1 + - - +
632G ILE 3.2 0.4 - - - -
633G LEU* 1.3 74.7 - - - +
635G ARG* 1.3 65.6 + - - +
636G LEU 3.2 0.4 + - - -
637G LEU* 3.7 6.6 + - - +
638G GLN* 3.1 36.8 - - - +
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Residues in contact with ARG 635 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 4.7 8.9 - - - -
631G LYS 3.5 11.2 + - - +
632G ILE* 3.4 44.5 + - - +
634G HIS* 1.3 79.1 - - - +
636G LEU* 1.3 73.3 + - - +
638G GLN* 3.6 12.4 + - - +
639G GLU* 3.1 50.4 + - - +
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Residues in contact with LEU 636 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 4.1 18.4 - - + -
280C VAL* 3.5 39.2 - - + +
281C GLU* 5.0 1.0 - - - +
284C LYS* 2.7 33.7 + - - -
450C PHE* 3.5 23.1 - - + -
632G ILE* 3.0 33.8 + - + +
633G LEU 3.8 4.5 - - - +
634G HIS 3.2 0.2 - - - -
635G ARG* 1.3 97.6 - - + +
637G LEU* 1.3 52.0 + - - +
638G GLN* 2.7 8.8 + - - -
639G GLU* 4.2 9.6 + - - +
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Residues in contact with LEU 637 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C VAL* 4.9 6.3 - - + +
283C ALA* 5.9 0.2 - - + -
284C LYS* 3.8 21.4 + - + +
289C PHE* 3.5 16.6 - - + -
290C SER* 5.5 2.7 - - - +
294C LEU* 3.6 24.8 - - + +
297C GLN* 3.0 52.1 + - + +
298C VAL* 3.9 14.1 - - + +
301C LEU* 3.8 23.1 - - + -
633G LEU* 3.3 14.5 + - + +
634G HIS* 3.7 2.2 + - - +
635G ARG 3.6 0.6 - - - -
636G LEU* 1.3 74.2 - - - +
638G GLN* 1.3 62.6 + - - +
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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