Contacts of the helix formed by residues 238 - 244 (chain D) in PDB entry 5COX
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 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C GLU* 3.7 24.7 - - - +
144C ASN* 6.0 0.4 - - - +
671C NAG 4.4 38.8 - - - +
237D THR* 1.3 69.0 - - - +
239D ASP* 1.3 66.7 + - - +
241D GLN* 3.9 19.3 - - + +
242D HIS* 3.2 65.7 + - + +
245D ARG* 5.1 0.2 - - - +
326D GLU* 5.4 2.0 - - - +
330D GLN* 6.1 1.1 - - - +
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Residues in contact with ASP 239 (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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237D THR* 3.0 10.8 + - - +
238D LEU* 1.3 86.0 - - + +
240D ARG* 1.3 61.6 + - - +
242D HIS* 3.4 5.3 + - - +
243D LYS* 3.3 43.5 + - - +
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Residues in contact with ARG 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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235D GLY* 3.7 15.3 - - - -
236D GLU* 2.9 30.3 + - - +
237D THR* 2.8 22.7 + - - +
239D ASP* 1.3 77.4 - - - +
241D GLN* 1.3 57.9 + - - +
242D HIS 3.0 1.6 - - - -
243D LYS* 2.7 34.7 + - - +
244D LEU* 3.1 18.4 + - + +
271D VAL* 2.9 26.0 - - + +
272D GLU* 2.9 25.7 + - - +
273D MET* 3.4 23.2 - - - -
288D GLY* 3.4 15.3 + - - -
289D GLN 3.4 22.4 - - - +
290D GLU* 3.5 7.7 + - - +
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Residues in contact with GLN 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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140C GLU* 5.0 3.6 + - - -
234D TYR* 3.1 28.1 + - + +
235D GLY 4.9 2.0 - - - +
237D THR 2.7 16.1 + - - +
238D LEU* 3.6 26.4 - - + +
240D ARG* 1.3 73.4 - - - +
242D HIS* 1.3 64.4 + - - +
244D LEU* 3.2 4.1 + - - +
245D ARG* 2.6 61.4 + - - +
252D LEU* 5.1 1.2 - - - +
329D PHE* 3.0 32.9 - - + -
330D GLN* 4.6 6.9 - - - +
333D LYS* 4.6 14.5 - - - +
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Residues in contact with HIS 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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671C NAG 5.7 1.8 - - - -
238D LEU* 3.2 53.7 + - + +
239D ASP* 3.7 7.2 - - - +
240D ARG 3.0 1.2 - - - -
241D GLN* 1.3 80.4 - - - +
243D LYS* 1.3 63.5 + - - +
244D LEU 3.4 0.3 + - - -
245D ARG* 3.3 37.3 + - - +
247D PHE* 3.3 44.5 - + + -
253D LYS* 4.8 0.2 + - - -
326D GLU* 4.2 6.1 - - - -
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Residues in contact with LYS 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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239D ASP* 3.3 34.3 + - - +
240D ARG* 2.7 14.8 + - - +
242D HIS* 1.3 73.1 - - + +
244D LEU* 1.3 51.8 + - - +
253D LYS* 2.5 26.9 + - - -
269D THR* 3.1 36.4 - - - +
270D GLN* 3.5 23.3 + - + +
271D VAL* 3.7 19.4 - - + +
272D GLU* 4.8 6.3 - - - +
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Residues in contact with LEU 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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233D ILE 4.3 4.9 - - - +
234D TYR 3.2 32.5 - - - +
240D ARG* 3.1 20.2 + - + +
241D GLN* 3.5 6.7 - - - +
242D HIS 3.1 0.2 - - - -
243D LYS* 1.3 77.1 - - - +
245D ARG* 1.3 48.5 + - - +
252D LEU* 3.1 17.3 - - + +
253D LYS* 2.8 44.0 + - - +
264D PRO* 5.3 3.2 - - + +
269D THR* 4.8 1.6 - - + +
271D VAL* 3.5 28.5 - - + -
286D ALA* 4.2 18.4 - - + -
287D VAL 4.4 3.1 - - - +
288D GLY* 3.7 23.6 - - - +
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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