Contacts of the strand formed by residues 246 - 253 (chain J) in PDB entry 3DXA
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 GLN 246 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135J PRO* 4.3 18.7 - - + +
226J GLN* 2.9 5.8 + - - +
227J PHE* 2.7 47.3 + - + +
242J LYS 3.9 15.9 - - - +
244J VAL* 2.7 19.5 + - + +
245J THR* 1.3 73.6 - - - +
247J ILE* 1.3 63.5 + - - +
248J VAL* 3.4 28.9 - - + +
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Residues in contact with ILE 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J ARG* 5.5 0.4 - - - +
224J GLN* 3.4 43.3 - - + +
225J VAL 3.4 8.5 - - - +
226J GLN* 3.5 30.5 - - + +
246J GLN* 1.3 80.9 + - - +
248J VAL* 1.3 62.1 + - - +
249J SER* 4.0 6.8 + - - +
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Residues in contact with VAL 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J PRO* 3.2 35.2 - - + +
137J GLU* 4.3 0.9 - - - -
138J VAL* 3.3 40.7 - - + +
225J VAL* 2.8 34.4 + - - +
246J GLN* 3.4 28.0 - - + +
247J ILE* 1.3 70.9 - - - +
249J SER* 1.3 70.5 + - - +
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Residues in contact with SER 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J VAL* 4.1 8.2 - - - +
222J ARG* 3.7 23.8 + - - -
223J CYS 3.3 10.5 - - - -
224J GLN* 3.5 22.0 - - - +
247J ILE* 4.0 7.2 + - - +
248J VAL* 1.3 84.8 + - - +
250J ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J VAL* 3.6 27.8 - - + +
139J ALA* 3.6 17.7 - - - -
140J VAL* 3.8 14.1 - - + +
222J ARG* 3.5 4.2 - - - +
223J CYS* 3.0 33.5 + - + +
249J SER* 1.3 74.3 - - - +
251J GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 3.2 16.9 - - - +
109E ARG* 3.2 16.7 + - - -
138I ASP* 5.4 1.6 - - - +
140J VAL* 3.1 16.2 - - - +
220J HIS* 3.5 22.0 - - + +
221J PHE 3.4 4.9 - - - -
222J ARG* 4.5 6.6 - - - +
249J SER* 6.4 0.2 - - - -
250J ALA* 1.3 75.7 - - - +
252J ALA* 1.3 61.8 + - - +
253J TRP* 3.7 18.9 + - + +
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Residues in contact with ALA 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I ASP* 5.3 6.5 - - - +
140J VAL* 3.6 21.3 - - + -
142J GLU* 5.5 6.5 - - + +
156J LEU* 4.9 6.3 - - + -
214J TRP* 5.0 6.3 - - + -
220J HIS* 3.9 1.6 - - - -
221J PHE* 2.7 49.5 + - + +
251J GLU* 1.3 79.3 - - - +
253J TRP* 1.3 68.0 + - - +
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Residues in contact with TRP 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG* 3.1 68.1 - - - +
146A LYS* 5.7 5.8 - - - -
108E TYR* 5.7 2.9 - - - -
109E ARG* 3.6 29.6 - - + -
110E ASP* 6.1 1.6 - - - -
142J GLU* 4.8 2.1 - - - +
214J TRP* 3.2 22.8 - - - -
217J PRO 4.6 3.6 - - - -
218J ARG* 4.2 16.6 - - - -
219J ASN 3.6 5.8 - - - -
220J HIS* 3.4 39.4 - + + -
221J PHE* 4.2 0.4 - - - -
251J GLU* 3.7 18.4 + - + -
252J ALA* 1.3 81.9 - - - +
254J GLY* 1.3 68.2 + - - +
255J ARG* 4.6 2.8 - - - +
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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