Contacts of the helix formed by residues 224 - 228 (chain D) in PDB entry 3DLX
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 ARG 224 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C GLU* 4.3 4.0 - - - +
213D TRP* 3.6 58.1 - - + +
223D PHE* 1.3 72.9 - - - +
225D LYS* 1.3 93.1 + - + +
227D ALA* 3.1 23.6 + - + +
246D GLU* 5.5 0.9 - - - +
277D LYS* 4.2 7.5 - - - +
360D ASP* 3.1 38.1 + - - -
362D ASP* 2.8 39.0 + - - +
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Residues in contact with LYS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C GLU* 3.1 28.1 + - - +
223D PHE 5.1 0.3 - - - +
224D ARG* 1.3 100.1 + - + +
226D SER* 1.3 60.6 + - - +
227D ALA 3.2 2.6 + - - -
228D ARG* 3.7 13.5 + - - +
346D GLY 5.3 0.2 - - - +
358D GLU 5.6 0.8 + - - -
360D ASP* 3.0 34.1 + - - +
362D ASP* 3.3 10.3 - - + +
363D LEU* 4.1 25.3 - - + +
373D ILE* 6.2 2.2 - - - -
379D PHE* 3.5 42.5 - - + +
380D PHE 5.7 0.3 - - - +
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Residues in contact with SER 226 (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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64D PHE* 5.2 0.2 - - - +
67D CYS* 3.8 7.4 - - - -
225D LYS* 1.3 70.3 - - - +
227D ALA* 1.3 54.5 + - - +
228D ARG* 3.2 6.6 + - - -
229D ASN* 3.0 24.6 + - - +
345D ASN* 3.5 32.4 + - - +
346D GLY 5.0 1.6 - - - -
347D VAL* 3.7 20.0 - - - -
362D ASP 2.7 24.7 + - - -
363D LEU* 4.5 1.1 - - - -
364D ILE 3.2 19.7 + - - -
379D PHE* 3.7 6.1 - - - -
380D PHE 6.0 0.4 - - - -
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Residues in contact with ALA 227 (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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67D CYS* 3.7 7.9 - - - -
68D GLY* 3.9 15.6 - - - -
211D LYS* 4.4 5.3 - - + +
223D PHE* 4.4 5.9 - - - -
224D ARG* 3.1 20.2 + - + +
226D SER* 1.3 74.7 - - - +
228D ARG* 1.3 59.6 + - - +
229D ASN* 3.4 8.0 + - - +
231D ASN* 2.9 24.3 + - - +
362D ASP* 3.6 24.2 + - - +
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Residues in contact with ARG 228 (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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257C GLU* 3.0 39.2 + - - +
223D PHE* 3.6 33.7 + - + +
225D LYS 3.7 11.1 + - - +
226D SER* 3.2 1.2 - - - -
227D ALA* 1.3 77.9 - - - +
229D ASN* 1.3 55.2 + - - +
231D ASN* 2.7 38.1 + - - +
232D LEU* 3.4 27.3 + - + +
260D HIS* 3.4 33.3 + - - -
379D PHE* 3.9 8.5 + - - +
380D PHE* 3.7 25.6 - - - +
381D SER* 3.7 26.4 - - - +
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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