Contacts of the helix formed by residues 23 - 36 (chain 1) in PDB entry 2D3O
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 23 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181 VAL* 3.7 17.0 - - + +
191 PRO 3.1 25.1 - - - +
201 ALA* 3.8 13.0 + - - +
211 ALA 3.6 2.2 + - - -
221 GLU* 1.3 78.4 - - - +
241 ASN* 1.3 69.4 + - - +
251 ARG 3.6 1.2 - - - +
261 ALA* 3.3 17.8 - - + +
271 TYR* 3.6 25.6 + - + -
991 GLY 6.1 0.9 - - - -
1001 GLN* 3.7 23.3 - - - +
1011 ALA* 4.7 1.8 - - - -
1021 PHE* 4.9 12.3 - - + +
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Residues in contact with ASN 24 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 ALA 4.5 6.4 + - - +
211 ALA 5.0 0.4 + - - -
231 VAL* 1.3 75.2 - - - +
251 ARG* 1.3 104.2 + - - +
261 ALA 3.0 5.5 + - - -
271 TYR* 3.1 16.2 + - - +
281 ASP* 2.5 32.4 + - - +
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Residues in contact with ARG 25 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 ALA 5.4 2.0 + - - -
211 ALA 4.7 16.8 + - - +
221 GLU* 6.1 2.2 - - - -
231 VAL 4.6 1.0 - - - +
241 ASN* 1.3 114.4 - - - +
261 ALA* 1.3 61.7 + - - +
281 ASP* 3.0 13.4 + - + +
291 GLN* 3.3 32.1 + - + +
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Residues in contact with ALA 26 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 GLU 4.0 8.7 - - - +
231 VAL* 3.3 26.9 - - + +
241 ASN 3.0 0.6 - - - -
251 ARG* 1.3 80.3 - - - +
271 TYR* 1.3 59.2 + - + +
291 GLN* 4.0 3.5 + - - +
301 VAL* 3.2 26.5 + - - +
661 VAL* 5.5 1.0 - - - +
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Residues in contact with TYR 27 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231 VAL* 3.6 26.4 + - + -
241 ASN* 3.1 8.7 + - - +
261 ALA* 1.3 77.6 - - + +
281 ASP* 1.3 60.5 + - - +
291 GLN 3.1 2.7 - - - -
301 VAL* 3.7 3.1 - - + +
311 TRP* 2.8 42.5 + + + +
621 VAL* 4.2 6.5 - - + -
631 GLU* 2.8 54.0 + - + +
661 VAL* 3.9 31.4 - - + -
961 VAL* 5.1 2.4 - - + +
1021 PHE* 4.6 14.4 - + - -
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Residues in contact with ASP 28 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241 ASN* 2.5 38.4 + - - +
251 ARG* 3.0 21.1 + - + +
271 TYR* 1.3 79.0 - - - +
291 GLN* 1.3 63.6 + - + +
311 TRP* 4.4 9.2 - - - -
321 ALA* 3.5 22.5 - - - +
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Residues in contact with GLN 29 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 ARG* 3.3 19.6 + - + +
261 ALA* 4.3 4.5 - - - +
271 TYR 3.1 0.2 - - - -
281 ASP* 1.3 83.8 - - - +
301 VAL* 1.3 61.0 + - + +
321 ALA* 4.9 0.4 - - - +
331 GLY* 3.2 22.0 + - - -
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Residues in contact with VAL 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261 ALA 3.2 21.1 - - - +
271 TYR* 3.2 4.1 + - - +
291 GLN* 1.3 80.7 - - + +
311 TRP* 1.3 56.5 + - - +
331 GLY* 4.7 0.4 - - - -
341 LEU* 2.5 70.4 + - + +
661 VAL* 3.8 27.1 - - + -
691 ARG* 3.9 31.0 - - - +
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Residues in contact with TRP 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271 TYR* 2.8 28.8 + + + +
281 ASP* 4.8 6.5 - - - -
301 VAL* 1.3 73.6 - - - +
321 ALA* 1.3 73.5 + - + +
341 LEU* 4.1 8.0 - - + +
351 ALA* 3.2 24.4 + - - +
501 ARG* 3.4 26.9 - - - -
531 ILE* 4.1 37.4 - - + +
541 GLU* 3.2 44.5 - - + +
581 GLY* 5.6 0.2 - - - -
621 VAL* 3.8 28.0 - - + +
661 VAL* 5.7 1.1 - - - +
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Residues in contact with ALA 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281 ASP 3.5 20.1 + - - +
291 GLN* 4.9 0.7 - - - +
301 VAL 3.4 0.2 - - - -
311 TRP* 1.3 89.3 - - + +
331 GLY* 1.3 56.7 + - - +
351 ALA* 3.7 6.9 + - - +
361 ARG* 2.6 62.0 + - - +
531 ILE* 6.3 0.2 - - - -
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Residues in contact with GLY 33 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291 GLN 3.2 19.7 + - - -
301 VAL* 3.1 4.1 + - - -
321 ALA* 1.3 76.2 - - - +
341 LEU* 1.3 64.0 + - - +
361 ARG* 3.4 18.4 + - - +
371 ASP* 3.1 18.6 - - - +
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Residues in contact with LEU 34 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301 VAL* 2.5 59.3 + - + +
311 TRP* 4.1 6.7 - - + +
331 GLY* 1.3 70.3 - - - -
351 ALA* 1.3 61.0 + - - +
361 ARG 3.0 2.5 - - - -
371 ASP* 2.9 10.4 + - - +
381 VAL* 2.8 46.2 + - + +
611 TYR 5.6 5.8 - - - +
651 GLN* 5.6 6.7 - - + -
661 VAL* 4.9 7.9 - - + -
691 ARG* 5.1 10.3 - - - +
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Residues in contact with ALA 35 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 TRP 3.2 19.3 + - - +
321 ALA* 3.8 9.6 - - - +
341 LEU* 1.3 77.6 - - - +
361 ARG* 1.3 59.1 + - + +
371 ASP 3.1 4.0 + - - -
381 VAL* 4.0 16.4 - - - +
431 PHE* 5.4 9.3 - - + -
451 PRO* 5.0 7.1 - - - +
461 GLY 5.4 1.0 + - - -
481 ALA* 4.9 9.4 - - + -
531 ILE* 4.4 29.4 - - + -
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Residues in contact with ARG 36 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 ALA* 2.6 46.0 + - - +
331 GLY* 3.7 11.4 - - - +
341 LEU 3.0 1.4 - - - -
351 ALA* 1.3 78.6 - - + +
371 ASP* 1.3 69.4 + - - +
451 PRO* 5.1 9.9 - - - +
461 GLY* 5.5 9.0 - - - +
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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