Contacts of the helix formed by residues 353 - 360 (chain C) 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 LEU 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C ILE* 3.7 25.8 - - + +
311C ALA* 6.0 0.4 - - - -
314C SER* 3.2 25.6 - - - +
349C VAL* 2.8 23.8 + - + +
352C GLU* 1.3 86.7 - - + +
354C VAL* 1.3 55.7 + - - +
355C SER 3.4 0.9 - - - -
356C LYS* 3.4 1.6 + - - +
357C MET* 2.9 42.5 + - + +
421C ARG* 5.0 13.0 - - + +
424C ALA* 4.8 4.0 - - + -
425C LEU* 4.3 28.0 - - + +
428C ILE* 4.0 25.6 - - + -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C SER* 3.2 34.7 + - - +
317C SER* 3.6 31.2 - - - +
318C ILE* 4.0 3.4 - - - +
320C VAL 5.0 0.4 - - - +
323C GLY 5.1 0.4 - - - +
324C ILE* 4.2 3.6 - - + -
349C VAL 2.9 11.7 + - - +
350C LEU* 3.6 38.8 - - + -
353C LEU* 1.3 72.1 - - - +
355C SER* 1.3 68.0 + - - +
357C MET* 3.5 4.1 + - - +
358C ARG* 3.2 37.4 + - - +
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Residues in contact with SER 355 (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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350C LEU 2.8 20.5 + - - -
351C THR* 3.5 18.6 + - - -
354C VAL* 1.3 76.7 - - - +
356C LYS* 1.3 63.9 + - - +
358C ARG* 3.0 18.6 + - - +
359C ASP* 3.0 37.1 + - - +
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Residues in contact with LYS 356 (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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351C THR 4.0 8.3 - - - +
352C GLU* 3.4 25.6 - - - +
353C LEU 3.4 2.9 + - - +
355C SER* 1.3 76.8 + - - +
357C MET* 1.3 68.3 + - - +
358C ARG 3.1 0.7 + - - -
359C ASP* 3.4 14.6 + - + +
360C MET* 3.3 21.8 + - + +
421C ARG* 3.9 37.1 - - - +
278D ARG* 4.2 13.2 - - - +
282D ASP* 2.8 39.6 + - - -
285D GLN* 5.4 0.2 - - - +
286D GLU* 5.8 1.8 + - - -
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Residues in contact with MET 357 (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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311C ALA* 3.8 11.4 - - + +
314C SER* 3.8 14.4 - - - +
315C HIS* 3.5 34.5 - - + -
318C ILE* 3.4 17.8 - - + +
353C LEU* 2.9 33.8 + - + +
354C VAL* 3.8 1.6 - - - +
356C LYS* 1.3 73.2 - - + +
358C ARG* 1.3 61.2 + - - +
360C MET* 3.8 2.9 + - - -
361C GLN 3.6 1.4 + - - -
362C MET* 3.2 50.8 + - + +
367C LEU* 3.5 32.5 - - + -
421C ARG* 5.5 9.6 - - + +
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Residues in contact with ARG 358 (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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318C ILE* 3.0 42.8 + - + +
320C VAL 2.6 30.7 + - - -
321C LYS* 3.9 31.2 - - - +
322C ASP 5.3 0.8 - - - +
354C VAL* 3.2 28.1 + - - +
355C SER* 3.0 19.5 + - - +
356C LYS 3.0 0.8 - - - -
357C MET* 1.3 75.4 - - - +
359C ASP* 1.3 64.5 + - - +
360C MET 2.7 17.2 + - - -
361C GLN* 2.8 21.3 + - - +
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Residues in contact with ASP 359 (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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355C SER* 3.0 31.7 + - - +
356C LYS* 3.4 12.1 + - + +
358C ARG* 1.3 83.1 - - - +
360C MET* 1.3 58.7 + - + +
361C GLN* 3.7 0.7 - - - -
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Residues in contact with MET 360 (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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356C LYS* 3.3 19.1 - - - +
357C MET* 4.1 3.1 - - - +
358C ARG 2.7 4.6 + - - -
359C ASP* 1.3 75.3 - - + +
361C GLN* 1.3 67.4 + - - +
362C MET* 2.9 16.7 + - + -
411C GLN* 5.5 1.1 - - - +
414C ARG* 2.8 34.9 + - - +
417C LYS* 4.0 40.4 - - + +
418C LEU* 3.3 39.9 - - + +
421C ARG* 6.3 4.0 - - + -
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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