Contacts of the helix formed by residues 299 - 304 (chain B) in PDB entry 1D8D
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 CYS 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A ZN 2.3 36.3 - - - -
297B ASP* 2.9 16.0 + - - -
298B GLY* 1.3 72.0 - - - -
300B TYR* 1.3 72.5 + - - +
301B SER 3.0 0.2 - - - -
302B PHE 3.0 15.4 + - - -
303B TRP* 3.3 13.7 + - - +
361B TYR* 3.2 37.2 - - + +
362B HIS* 3.6 9.1 - - + -
365B TYR* 3.7 23.1 - - + +
366B CYS 4.9 0.4 - - - +
1000B FII 5.3 0.2 - - - -
8P CYS* 4.0 2.5 - - - -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B HIS* 3.2 28.4 + + - -
250B GLY 4.6 2.5 - - - -
288B PHE* 3.7 14.7 - - + +
289B GLN* 3.6 2.9 - - - -
290B GLY* 3.3 35.7 - - - -
295B LEU 4.7 1.3 - - - -
297B ASP* 3.1 40.9 + - + +
299B CYS* 1.3 82.1 - - - +
301B SER* 1.3 60.7 + - - +
302B PHE 2.8 6.5 - - - -
303B TRP* 3.8 29.6 - + + +
304B GLN* 2.9 40.1 + - + +
305B ALA 3.4 1.6 + - - -
1000B FII 2.6 41.0 + - + +
8P CYS* 5.1 1.9 - - - -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PHE* 4.7 2.1 + - - +
297B ASP 4.0 1.3 + - - -
298B GLY* 2.6 29.2 + - - -
300B TYR* 1.3 78.0 - - - +
302B PHE* 1.3 56.3 + - - +
305B ALA* 3.1 22.4 - - - +
306B GLY 4.2 0.5 + - - -
335B LEU* 3.6 28.3 - - - +
338B TYR* 5.0 1.2 - - - -
339B ILE* 3.6 27.8 - - - +
365B TYR 4.1 3.6 - - - -
366B CYS 4.6 0.2 - - - -
369B GLY* 3.2 21.2 - - - -
372B ILE* 5.1 1.0 - - - +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TYR* 6.1 0.2 - - - -
253B PHE* 3.6 44.1 - + - -
299B CYS 3.0 7.5 + - - +
300B TYR 2.8 1.0 - - - -
301B SER* 1.3 79.2 - - - +
303B TRP* 1.3 82.3 + + - +
304B GLN 3.2 1.1 - - - -
306B GLY* 2.8 28.6 + - - +
365B TYR* 3.6 40.1 + + + +
368B SER* 3.6 21.8 - - - -
369B GLY* 4.2 1.1 - - - +
372B ILE* 4.4 20.0 - - + -
397B THR* 4.7 0.9 - - + -
398B HIS 4.9 1.3 - - - -
399B PRO 4.3 6.3 - - - -
402B ASN* 3.5 38.4 - - + -
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TRP* 5.3 0.2 - + - -
154B TYR* 5.7 2.9 - - - -
205B TYR* 5.4 0.7 - + - -
249B GLY 3.7 19.1 - - - +
250B GLY* 4.3 0.4 - - - -
253B PHE* 3.5 56.7 - + + +
299B CYS* 3.3 23.2 + - - +
300B TYR* 3.8 16.2 - + + -
302B PHE* 1.3 90.7 - + - +
304B GLN* 1.3 62.7 + - - +
307B LEU* 3.5 11.1 + - - +
361B TYR* 2.8 28.9 + + - -
365B TYR* 3.4 42.9 - + - -
1000B FII 3.6 64.5 - - + +
10P ILE* 4.8 2.9 - - + -
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLY* 3.4 19.1 - - - -
276B TRP* 3.4 21.4 - - - -
277B VAL* 3.4 11.0 - - + +
280B ARG* 3.4 22.1 - - - +
288B PHE* 3.4 18.8 - - + -
289B GLN 3.0 28.0 + - - +
290B GLY 3.3 20.0 + - - -
300B TYR* 2.9 26.2 + - + +
303B TRP* 1.3 73.2 - - - +
305B ALA* 1.3 67.9 + - - +
306B GLY 3.1 0.9 - - - -
307B LEU* 2.8 30.9 + - - +
308B LEU 4.1 0.3 + - - -
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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