Contacts of the strand formed by residues 241 - 247 (chain A) in PDB entry 4J23
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 ASN 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A TRP* 4.1 9.9 + - - +
230A THR* 3.9 11.1 - - - +
231A CYS* 2.8 24.5 - - - +
232A VAL* 3.5 15.9 - - + +
239A SER* 4.9 2.4 + - - -
240A ILE* 1.3 89.4 + - - +
242A HIS* 1.3 69.3 + - - +
243A THR* 4.3 5.0 - - - +
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 5.8 1.6 - - + -
162A MET* 3.4 53.4 + - + +
165A ARG* 4.0 31.2 + - + +
179A CYS* 4.4 5.2 - - - -
230A THR* 3.0 6.9 - - - +
231A CYS* 2.7 40.3 + - + +
241A ASN* 1.3 79.9 + - - +
243A THR* 1.3 79.2 + - - +
244A TYR* 3.6 34.9 - + - -
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 4.4 19.5 + - - +
228A ASN* 5.0 9.4 + - + +
229A TYR 3.2 6.5 - - - -
230A THR* 2.8 31.6 - - + +
241A ASN* 4.3 5.8 - - - +
242A HIS* 1.3 90.8 + - - +
244A TYR* 1.3 64.2 - - - +
245A HIS 4.2 1.0 + - - -
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS 3.3 21.7 + - - -
162A MET* 3.3 13.7 - - - +
164A LYS* 3.5 30.3 - - + -
165A ARG* 3.5 10.1 - - - +
167A HIS* 4.4 2.9 - + - -
177A PHE* 3.9 45.5 - + + -
178A ARG 2.7 34.3 + - - -
179A CYS* 4.0 13.2 - - - -
191A TRP* 4.8 3.8 - + - -
227A GLY 3.3 2.3 - - - +
228A ASN* 3.2 2.5 - - - -
229A TYR* 2.5 51.0 + - + +
242A HIS* 3.6 28.3 - + + -
243A THR* 1.3 74.1 - - - +
245A HIS* 1.3 59.7 + - - +
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Residues in contact with HIS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 3.2 10.5 + - - +
166A LEU* 3.2 29.0 - - + +
167A HIS* 3.3 12.5 + - - +
177A PHE* 4.9 0.6 - - - -
226A LYS* 4.4 7.9 - - + -
227A GLY* 3.0 18.9 - - - -
228A ASN* 3.0 34.2 + - - +
243A THR 4.2 1.8 + - - -
244A TYR* 1.3 73.4 - - - +
246A LEU* 1.3 92.5 + - - +
247A ASP* 4.1 14.5 + - - -
52B ARG* 5.2 5.6 + - - -
154B SER* 4.6 24.0 + - - -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A HIS 3.8 9.0 - - - +
169A VAL* 5.5 2.2 - - + +
175A VAL* 4.4 18.6 - - + -
177A PHE* 3.6 31.9 - - + -
218A MET 5.5 1.6 - - - +
221A VAL* 5.3 6.3 - - + -
222A VAL 5.5 0.2 - - - +
225A ASP* 4.3 11.0 - - + +
226A LYS* 3.6 7.0 - - - +
227A GLY 2.7 26.1 + - - +
229A TYR* 3.9 27.4 - - + -
245A HIS* 1.3 81.2 + - - +
247A ASP* 1.3 63.5 + - - +
248A VAL* 3.3 32.3 - - + +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.0 19.0 - - + +
167A HIS 3.1 11.2 + - - -
168A ALA* 3.1 31.0 - - + +
169A VAL 3.2 6.3 + - - -
226A LYS* 2.5 30.4 + - - +
245A HIS* 4.2 9.9 + - - +
246A LEU* 1.3 74.3 - - - +
248A VAL* 1.3 65.4 + - - +
249A VAL* 3.6 2.8 + - - +
52B ARG* 5.1 11.1 + - - -
150B LEU* 3.7 23.8 - - + +
151B PRO* 5.5 4.4 - - - +
153B SER 5.3 1.6 - - - +
154B SER* 5.4 5.2 - - - -
155B ASP 6.0 0.9 - - - -
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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