Contacts of the helix formed by residues 284 - 289 (chain Q) in PDB entry 2D2I
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 VAL 284 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282Q PRO 5.2 0.2 - - - +
283Q LEU* 1.3 79.5 - - - +
285Q SER* 1.3 68.3 + - - +
286Q SER* 4.8 0.2 - - - -
287Q ASP* 2.6 40.3 + - - +
288Q PHE* 3.7 9.5 - - - -
315Q TRP* 4.3 3.1 - - - -
199R ARG* 4.0 9.4 - - - +
202R ARG* 3.5 42.2 - - + +
207R ASN* 3.4 23.6 - - - +
208R ILE 3.6 8.7 - - - +
209R VAL* 3.8 27.4 - - + -
210R PRO* 4.4 1.6 - - + -
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Residues in contact with SER 285 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239Q THR* 4.8 4.0 - - - +
241Q ASN 5.3 1.3 - - - -
242Q VAL* 3.5 33.3 - - - +
284Q VAL* 1.3 72.6 - - - +
286Q SER* 1.3 64.4 + - - +
288Q PHE* 3.0 14.5 + - - +
315Q TRP* 3.6 28.6 - - - -
206R VAL 4.4 1.0 + - - -
207R ASN* 3.3 7.8 - - - -
208R ILE* 2.7 43.3 + - - +
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Residues in contact with SER 286 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O ASP 5.6 0.2 - - - -
51O SER* 3.9 29.5 + - - -
242Q VAL* 5.4 0.4 - - - -
284Q VAL* 4.8 1.8 - - - -
285Q SER* 1.3 76.2 + - - +
287Q ASP* 1.3 62.4 + - - +
288Q PHE 3.1 1.4 + - - -
289Q ARG* 3.2 42.9 + - - +
206R VAL* 3.3 14.4 + - - +
207R ASN* 2.9 26.6 + - - -
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Residues in contact with ASP 287 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O TYR* 3.7 17.4 - - + +
50O ASP 4.6 2.8 + - - +
54O GLY 6.1 0.5 - - - -
55O ARG 6.0 0.2 + - - -
283Q LEU* 3.4 31.0 - - + +
284Q VAL* 2.6 42.8 + - - +
286Q SER* 1.3 78.0 - - - +
288Q PHE* 1.3 63.8 + - + +
289Q ARG 3.5 2.5 + - - +
291Q THR* 4.4 1.9 + - - -
202R ARG* 3.0 32.1 + - - -
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Residues in contact with PHE 288 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242Q VAL* 4.5 11.7 - - + -
277Q LYS* 5.3 6.5 - - + -
279Q SER* 4.0 11.9 - - - -
283Q LEU* 3.8 35.9 - - + -
284Q VAL 3.7 17.3 - - - -
285Q SER 3.0 11.2 + - - +
287Q ASP* 1.3 80.8 - - - +
289Q ARG* 1.3 64.6 + - - +
290Q GLY 3.2 0.5 + - - -
291Q THR* 2.8 31.0 + - + +
296Q ILE* 3.7 39.7 - - + -
298Q ASP* 4.9 1.3 - - - -
315Q TRP* 3.2 52.9 - + + -
317Q ASP* 3.7 9.2 - - - +
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Residues in contact with ARG 289 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O ASP 4.4 0.6 + - - -
51O SER 3.2 30.0 + - - -
52O VAL 4.6 4.2 + - - -
54O GLY* 4.2 19.6 - - - +
289O ARG* 3.3 27.7 - - - +
52Q VAL* 4.4 23.0 + - + +
241Q ASN* 4.7 8.7 - - + +
242Q VAL* 4.0 17.7 - - + +
285Q SER 4.2 1.0 + - - -
286Q SER* 3.2 32.8 + - - +
287Q ASP 3.5 3.0 - - - +
288Q PHE* 1.3 77.8 - - - +
290Q GLY* 1.3 60.4 + - - +
291Q THR* 3.3 1.6 + - - -
317Q ASP* 3.4 5.8 - - - +
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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