Contacts of the helix formed by residues 286 - 292 (chain C) in PDB entry 1DVM
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.6 5.8 - - + -
34C PHE* 3.8 19.5 - - + -
39C VAL* 3.9 29.2 - - + -
42C VAL* 5.3 1.1 - - + -
43C LEU* 5.0 2.2 - - + -
165C LEU* 4.6 11.0 - - + -
167C ASN* 5.5 0.2 - - + -
284C VAL* 3.1 26.0 + - + +
285C ASP* 1.3 69.6 - - - +
287C ARG* 1.3 56.6 + - - +
289C PRO* 3.1 9.7 - - + +
290C LEU* 2.8 44.3 + - + +
320C ALA* 2.8 27.8 + - + +
321C LEU 4.0 19.7 - - - +
322C GLN* 4.1 9.4 - - + -
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Residues in contact with ARG 287 (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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285C ASP* 3.0 29.5 + - - +
286C LEU* 1.3 72.9 - - - +
288C LYS* 1.3 72.1 + - + +
290C LEU* 2.8 5.9 + - - +
291C GLU* 2.8 39.8 + - - +
299C PHE* 3.6 57.9 + - + +
300C ARG* 3.7 24.2 - - - +
320C ALA* 4.3 1.6 - - - +
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Residues in contact with LYS 288 (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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285C ASP* 4.3 2.4 + - - +
287C ARG* 1.3 84.5 - - + +
289C PRO* 1.4 72.6 - - + +
291C GLU* 3.1 18.5 + - - +
292C ASN* 3.0 38.6 + - - +
217D ASP* 4.1 34.2 + - - +
219D HIS* 4.4 13.7 - - - -
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Residues in contact with PRO 289 (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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19C VAL* 4.1 21.2 - - + +
22C GLN* 3.8 28.4 - - + +
23C VAL* 4.4 21.5 - - + -
26C ALA* 6.1 2.2 - - + -
284C VAL* 5.7 2.9 - - + -
285C ASP 3.3 19.1 - - - +
286C LEU* 3.1 17.5 - - + +
287C ARG 3.3 0.2 - - - -
288C LYS* 1.4 98.0 - - + +
290C LEU* 1.3 60.6 + - - +
292C ASN* 4.0 1.5 + - - +
293C LEU* 3.7 20.3 + - - +
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Residues in contact with LEU 290 (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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15C PHE* 4.1 7.0 - - + -
19C VAL* 3.9 24.9 - - + -
39C VAL* 4.4 9.4 - - + -
43C LEU* 4.0 28.3 - - + -
165C LEU* 5.9 0.2 - - + -
286C LEU* 2.8 38.4 + - + +
287C ARG 3.5 2.2 - - - +
289C PRO* 1.3 77.0 - - + +
291C GLU* 1.3 64.9 + - - +
292C ASN 3.3 0.4 - - - -
293C LEU* 3.1 11.1 + - - +
295C MET* 3.1 47.3 + - + +
298C MET* 4.3 5.8 - - + -
299C PHE* 4.0 21.3 - - + -
320C ALA* 4.9 2.5 - - + -
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Residues in contact with GLU 291 (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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287C ARG* 2.8 37.4 + - - +
288C LYS* 3.6 24.4 - - - +
290C LEU* 1.3 73.4 - - - +
292C ASN* 1.3 59.4 + - - +
293C LEU 2.9 5.4 - - - -
294C GLY* 2.8 24.3 + - - -
295C MET 3.8 8.3 - - - +
296C THR* 3.5 19.6 - - + +
299C PHE* 3.8 14.8 - - + -
300C ARG* 2.5 39.8 + - - -
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Residues in contact with ASN 292 (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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22C GLN* 2.9 35.5 + - - +
25C GLN* 5.0 0.9 + - - -
288C LYS* 3.0 24.4 + - - +
289C PRO* 4.2 1.7 - - - +
290C LEU 3.3 0.4 - - - -
291C GLU* 1.3 80.4 - - - +
293C LEU* 1.3 61.5 + - - +
294C GLY 3.2 1.5 + - - -
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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