Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 4KG8
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 TYR 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A HIS* 3.4 25.4 - + + +
98A LEU 3.1 18.8 - - - +
99A THR* 4.2 2.9 - - + -
114A TRP* 3.3 9.3 - - - -
144A TYR* 3.6 17.5 - + - -
145A SER* 2.8 26.3 + - - -
146A LYS* 2.9 54.0 + - + +
202A PHE* 4.5 0.9 - + - -
231A THR* 3.6 26.9 - - - -
233A SER* 1.3 80.6 - - - +
235A PHE* 1.3 54.7 + - - +
180C LEU* 3.6 27.8 - - + +
203C LEU* 4.2 3.1 - - - +
204C GLY 2.9 38.7 + - - -
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Residues in contact with PHE 235 (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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97A HIS* 4.6 0.4 - - - -
98A LEU* 2.6 47.8 + - + +
114A TRP* 3.7 35.0 - + + -
131A GLY 3.8 13.0 - - - -
133A LEU* 3.4 32.5 - - + -
143A ILE* 5.3 2.9 - - + -
144A TYR* 3.4 14.6 - - - -
166A LEU* 3.4 21.5 - - + -
215A VAL* 3.3 39.0 - - + -
216A VAL* 4.5 0.7 - - - -
217A VAL* 3.4 22.7 - - + -
234A TYR* 1.3 79.1 - - - +
236A GLY* 1.3 62.1 + - - +
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Residues in contact with GLY 236 (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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96A ALA 3.1 15.0 - - - -
133A LEU* 4.3 6.3 - - - -
143A ILE* 3.5 2.9 - - - +
144A TYR* 3.0 48.2 + - - +
235A PHE* 1.3 81.1 - - - +
237A ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 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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95A ALA* 3.1 3.4 - - - +
96A ALA* 2.9 32.6 + - - +
126A LEU* 4.3 17.7 - - + -
133A LEU* 4.4 9.2 - - + +
141A TYR* 4.4 7.6 - - + -
142A TYR 3.1 13.5 - - - +
143A ILE* 3.9 17.3 - - + -
144A TYR* 3.6 4.6 - - - -
209A LEU* 6.5 0.2 - - + -
236A GLY* 1.3 75.7 - - - +
238A PHE* 1.3 67.3 + - - +
206C VAL* 5.3 0.9 - - - +
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Residues in contact with PHE 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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93A ASN* 4.4 0.4 - - - +
94A PRO 3.3 11.7 - - - +
95A ALA* 3.8 2.9 - - + -
141A TYR* 3.7 7.2 - - - -
142A TYR* 2.9 60.6 + + + -
144A TYR* 4.6 1.8 - + - -
237A ALA* 1.3 77.9 - - - +
239A MET* 1.3 76.7 + - - +
240A VAL* 3.5 20.4 - - + -
238B PHE* 3.9 15.0 - + - -
142C TYR* 3.7 9.4 - + - -
206C VAL* 3.5 31.9 - - + -
238C PHE* 4.1 9.2 - + - -
240C VAL* 3.5 42.6 - - + -
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Residues in contact with MET 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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93A ASN* 2.8 39.8 + - - +
94A PRO* 2.9 25.4 + - + +
137A LYS* 3.7 39.0 - - - +
138A ALA 3.9 18.4 - - - +
139A GLY* 4.2 10.8 - - - -
140A TYR 3.4 13.5 - - - +
141A TYR* 3.6 20.2 - - + -
238A PHE* 1.3 80.9 - - - +
240A VAL* 1.3 72.2 + - - +
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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