Contacts of the helix formed by residues 239 - 244 (chain D) in PDB entry 5EIB
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 THR 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.7 14.8 - - + -
52D TYR* 3.5 25.8 - - - +
136D GLN* 4.4 1.6 - - - +
167D ASN* 5.9 0.2 - - - +
169D PHE* 4.0 22.9 - - + -
235D MET 3.0 19.7 + - - +
236D SER 3.3 2.3 + - - -
237D GLY 3.2 0.4 - - - -
238D VAL* 1.3 78.5 - - - +
240D THR* 1.3 64.8 + - - +
241D CYS 3.3 2.9 - - - -
242D LEU* 3.1 24.8 + - + +
243D ARG* 2.8 40.7 + - - +
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Residues in contact with THR 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER 3.1 15.9 + - - -
237D GLY 3.3 12.4 + - - -
238D VAL 3.5 0.4 - - - -
239D THR* 1.3 76.1 - - - +
241D CYS* 1.3 63.9 + - - +
243D ARG* 3.1 20.9 + - - +
244D PHE* 3.1 21.6 + - + +
318D ILE* 4.3 14.6 - - + -
320D ARG* 3.4 28.5 + - - +
356D CYS* 3.8 36.8 - - + -
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Residues in contact with CYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 3.1 18.4 + - - -
237D GLY 4.9 0.4 + - - -
238D VAL 4.9 4.4 + - - +
239D THR 3.3 0.8 - - - -
240D THR* 1.3 79.7 - - - +
242D LEU* 1.3 57.3 + - + +
243D ARG 3.4 0.2 - - - -
244D PHE 3.5 6.4 - - - +
246D GLY* 5.6 1.2 + - - -
248D LEU* 3.6 18.3 - - - +
249D ASN* 3.5 24.5 - - + +
250D ALA* 3.4 10.4 - - - +
318D ILE* 3.7 35.0 - - - -
354D ALA* 3.8 15.7 - - - -
356D CYS* 6.5 0.2 - - - -
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Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.1 3.6 - - + -
48D ARG* 3.4 13.8 + - - -
51D VAL* 3.4 28.2 - - + +
52D TYR* 3.6 25.4 - - + +
133D GLN* 4.9 2.8 + - - +
136D GLN* 5.1 0.7 - - - +
167D ASN* 5.4 2.7 - - - +
238D VAL 4.7 4.7 - - - +
239D THR* 3.1 25.5 + - + +
241D CYS* 1.3 78.5 - - + +
243D ARG* 1.3 61.6 - - + +
249D ASN 4.0 7.9 - - - +
250D ALA 3.7 4.7 - - - -
251D ASP* 3.7 35.2 - - - +
252D LEU* 3.6 29.4 - - + +
255D LEU* 5.3 8.5 - - + -
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.6 21.3 - - - +
27D GLU* 3.1 28.9 + - - -
28D HIS* 3.1 55.2 + - + +
42D LEU 4.8 0.7 - - - +
48D ARG* 3.5 24.4 + - - +
51D VAL* 5.1 0.2 - - - -
52D TYR* 3.4 38.6 - - + -
236D SER* 2.8 34.6 + - - +
239D THR* 2.8 25.2 + - - +
240D THR* 3.1 14.0 + - - +
242D LEU* 1.3 77.5 - - - +
244D PHE* 1.3 75.6 + - + +
245D PRO* 4.8 0.2 - - - +
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Residues in contact with PHE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 4.3 13.2 - - + -
28D HIS* 3.9 17.7 - + - -
42D LEU* 3.5 26.9 - - + -
45D GLN* 4.4 4.5 - - - -
48D ARG* 3.1 20.7 + - - +
240D THR* 3.1 27.6 + - + +
241D CYS* 3.5 8.7 - - - +
243D ARG* 1.3 106.8 - - + +
245D PRO* 1.3 78.2 - - + +
246D GLY* 3.6 0.5 + - - -
320D ARG* 3.7 22.7 - - - -
356D CYS* 4.0 18.6 - - - -
358D ILE* 4.1 26.0 - - + -
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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