Contacts of the helix formed by residues 448 - 455 (chain C) in PDB entry 1XVP
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 ASP 448 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C CYS* 5.2 1.3 + - - +
270C GLN* 4.5 22.2 + - - +
273C ASP* 3.0 34.7 - - + +
446C PRO 4.9 4.4 - - - +
447C ILE* 1.3 76.6 - - - +
449C THR* 1.3 60.4 + - - +
450C PHE 3.2 1.2 + - - -
451C LEU* 3.3 5.1 + - - +
452C MET* 2.8 32.4 + - - +
686F ARG* 3.2 40.3 + - - +
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Residues in contact with THR 449 (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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273C ASP* 5.4 0.3 + - - -
277C PHE* 5.3 3.8 - - - -
447C ILE 4.1 0.6 + - - -
448C ASP* 1.3 73.8 - - - +
450C PHE* 1.3 63.0 + - - +
452C MET* 3.6 6.7 - - - +
453C GLU* 3.3 21.8 + - - +
686F ARG* 3.9 24.0 - - - +
632G ILE* 4.1 18.9 - - - +
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Residues in contact with PHE 450 (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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273C ASP* 3.2 5.0 + - - +
276C LEU* 3.1 64.8 - - + +
277C PHE* 3.4 37.9 - + + -
280C VAL* 4.1 9.0 - - + -
449C THR* 1.3 79.9 + - - +
451C LEU* 1.3 67.8 + - - +
452C MET 3.2 0.4 - - - -
453C GLU* 3.4 15.0 + - - +
454C MET* 3.5 13.2 + - + +
632G ILE* 3.3 36.8 - - + -
633G LEU* 4.0 23.1 - - + -
636G LEU* 3.6 18.2 - - + -
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Residues in contact with LEU 451 (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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269C CYS* 3.0 44.9 - - + +
272C ALA* 3.8 23.3 - - + -
273C ASP* 2.6 26.6 + - + +
276C LEU* 3.7 9.4 - - + +
305C TRP* 4.3 22.7 - - + -
436C LEU* 4.8 14.4 - - + -
447C ILE* 4.3 17.0 - - + -
448C ASP 3.3 6.3 + - - +
450C PHE* 1.3 71.4 - - - +
452C MET* 1.3 63.9 + - - +
454C MET* 3.2 14.7 + - - +
455C LEU* 3.2 18.2 + - + +
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Residues in contact with MET 452 (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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331B GLN* 6.2 0.4 - - - +
348B SER* 5.8 4.3 - - - +
440C LYS* 3.3 40.1 + - + +
447C ILE* 3.6 28.5 - - + +
448C ASP 2.8 22.6 + - - +
449C THR* 3.6 8.1 - - - +
451C LEU* 1.3 78.3 - - - +
453C GLU* 1.3 57.6 + - - +
455C LEU* 3.2 28.8 - - - +
456C GLU* 3.8 4.2 - - - +
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Residues in contact with GLU 453 (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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449C THR 3.3 14.5 + - - +
450C PHE* 3.8 10.2 - - - +
451C LEU 3.3 1.0 - - - -
452C MET* 1.3 81.4 - - - +
454C MET* 1.3 63.8 + - - +
455C LEU 3.6 0.2 + - - -
456C GLU* 3.6 18.0 - - - +
629G ARG 4.2 12.3 - - - +
630G HIS* 3.1 50.3 + - + +
631G LYS 4.2 0.5 + - - -
632G ILE* 3.0 39.7 + - + +
633G LEU* 3.4 13.1 - - - +
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Residues in contact with MET 454 (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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276C LEU* 3.6 29.2 - - + -
301C LEU* 3.7 11.2 - - + -
302C ARG* 3.5 34.1 - - - +
305C TRP* 3.3 61.9 + - + +
450C PHE* 3.5 10.3 + - + +
451C LEU 3.2 9.5 + - - +
453C GLU* 1.3 87.3 - - - +
455C LEU* 1.3 59.4 + - - +
456C GLU* 4.7 2.0 - - - +
630G HIS* 4.3 7.4 + - - -
633G LEU* 3.9 25.8 - - + -
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Residues in contact with LEU 455 (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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305C TRP* 4.3 18.6 - - + -
433C LEU* 4.7 6.1 - - + -
436C LEU* 4.5 25.6 - - + +
437C PHE* 3.6 36.3 - - + -
440C LYS* 4.1 22.5 + - + -
447C ILE* 5.3 4.3 - - + -
451C LEU* 3.2 26.2 - - + +
452C MET* 3.2 19.0 - - - +
453C GLU 3.4 0.2 - - - -
454C MET* 1.3 80.5 - - - +
456C GLU* 1.3 76.9 + - - +
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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