Contacts of the strand formed by residues 236 - 240 (chain A) in PDB entry 3CB4
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A TYR* 5.1 5.1 - - - -
204A LEU* 3.9 26.1 - - - +
219A LYS* 4.4 11.2 - - - +
234A ALA 3.3 1.3 - - - -
235A ASP* 1.3 90.0 - - + +
237A LEU* 1.3 64.0 + - - +
244A GLN* 4.1 10.7 + - - -
246A ASP* 2.6 41.6 + - - +
257A TRP* 3.7 18.2 - - + -
258A LEU* 3.5 3.4 - - - +
259A VAL* 2.6 51.1 + - + +
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Residues in contact with LEU 237 (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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217A LEU* 3.7 45.5 - - + +
218A ARG 4.0 11.2 - - - +
219A LYS* 4.7 10.2 - - + +
234A ALA* 4.7 1.1 - - + -
236A ARG* 1.3 77.4 - - - +
238A GLY* 1.3 59.4 + - - +
246A ASP* 3.7 5.0 - - - +
247A ARG* 2.8 44.5 + - + +
248A THR 3.7 2.9 - - - +
249A GLU* 3.4 27.8 - - - +
250A LEU* 4.3 11.4 - - + +
257A TRP* 3.1 23.1 - - - +
258A LEU* 4.0 11.0 - - + -
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Residues in contact with GLY 238 (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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237A LEU* 1.3 76.2 - - - +
239A ILE* 1.3 63.6 + - - +
245A VAL 3.1 13.7 - - - -
247A ARG* 3.5 13.9 - - - -
250A LEU* 3.8 5.0 - - - +
256A GLY* 3.1 6.9 - - - -
257A TRP* 2.8 40.1 + - - +
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Residues in contact with ILE 239 (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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60A THR* 4.0 31.4 - - + +
72A GLN* 5.3 4.3 - - - +
238A GLY* 1.3 78.7 - - - +
240A PHE* 1.3 60.8 + - - +
241A THR* 4.2 13.2 - - - +
243A LYS 3.6 1.2 - - - +
244A GLN* 3.9 0.3 - - - -
245A VAL* 2.9 34.6 + - + +
247A ARG* 3.4 43.3 - - + +
250A LEU* 3.8 13.7 - - + -
254A GLU* 5.4 1.8 - - - +
255A VAL 3.6 20.6 - - - +
256A GLY* 4.3 3.6 - - - -
257A TRP* 3.2 9.0 + - - -
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Residues in contact with PHE 240 (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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58A SER* 3.4 36.1 - - - +
59A VAL* 3.6 1.1 - - - -
60A THR* 2.7 39.7 + - - -
199A TRP* 3.9 31.9 - + - -
207A VAL* 5.3 0.2 - - + -
209A LEU* 4.2 10.8 - - + -
239A ILE* 1.3 73.5 - - - +
241A THR* 1.3 58.0 + - - +
242A PRO* 3.5 17.9 - - - +
243A LYS 3.7 0.2 - - - -
244A GLN* 3.9 33.4 - - + -
256A GLY* 5.3 1.2 - - - -
257A TRP* 3.5 37.2 - + + -
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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