Contacts of the strand formed by residues 235 - 245 (chain A) in PDB entry 4K88
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 ALA 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLU* 5.0 4.7 - - + +
227A ALA 3.2 15.3 - - - +
228A PHE* 4.0 11.2 - - + +
229A ILE 5.1 0.4 - - - -
234A ARG* 1.3 76.1 - - - +
236A ILE* 1.3 63.2 + - - +
442A ILE* 4.3 7.8 - - + +
479A LEU* 3.9 33.0 - - + -
510A ARG 3.1 6.6 + - - +
511A SER* 3.5 22.3 - - - -
512A TYR* 3.6 9.6 + - - -
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Residues in contact with ILE 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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162A LEU* 3.6 30.7 - - + -
226A GLU* 3.4 7.7 - - - -
227A ALA* 2.6 46.7 + - + +
229A ILE* 4.1 16.2 - - + -
235A ALA* 1.3 77.1 - - - +
237A GLN* 1.3 72.5 + - - +
238A GLY* 3.6 0.4 + - - -
278A ARG* 3.9 28.5 - - + +
282A VAL* 3.9 34.3 - - + -
511A SER* 5.7 0.9 - - - -
512A TYR* 4.2 21.5 - - + +
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Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 4.5 0.2 + - - -
210A LYS* 2.9 38.0 + - - +
224A THR* 3.3 8.9 + - - +
225A ILE 3.7 3.8 - - - -
226A GLU* 3.5 11.8 + - - +
236A ILE* 1.3 78.2 - - - +
238A GLY* 1.3 60.6 + - - +
239A GLY* 4.4 3.4 - - - +
240A THR* 3.3 30.9 - - + +
278A ARG* 3.3 42.2 + - - +
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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
----------------------------------------------------------
197A TYR* 3.1 38.7 + - - -
225A ILE* 2.6 25.2 + - - -
227A ALA* 5.7 2.5 - - - -
236A ILE* 3.6 3.0 + - - -
237A GLN* 1.3 75.5 - - - +
239A GLY* 1.3 56.8 + - - +
275A LEU* 3.3 10.6 - - - +
276A THR 4.8 1.6 + - - -
278A ARG* 4.1 9.2 - - - -
282A VAL* 5.9 0.7 - - - -
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Residues in contact with GLY 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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190A LEU* 4.3 1.4 - - - +
193A TYR* 4.3 11.9 - - - -
224A THR* 3.4 4.2 + - - -
225A ILE* 3.2 33.7 + - - +
237A GLN* 3.9 1.3 - - - -
238A GLY* 1.3 75.9 - - - +
240A THR* 1.3 65.8 + - - -
274A GLY 3.6 12.3 - - - -
275A LEU* 4.2 7.9 - - - -
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 4.8 0.9 - - - -
193A TYR* 3.4 5.2 - - - -
210A LYS* 5.5 1.1 - - - +
222A THR* 4.7 2.5 - - + -
223A THR 3.7 7.4 - - - -
224A THR* 3.9 6.1 - - - +
237A GLN* 3.3 38.1 - - + +
239A GLY* 1.3 79.5 - - - +
241A SER* 1.3 62.0 + - - +
242A HIS* 2.8 33.9 + - + +
273A TRP* 3.3 4.9 - - - +
274A GLY* 3.1 36.3 + - - -
602A HFG 4.6 2.9 - - - +
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Residues in contact with SER 241 (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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186A VAL* 2.9 38.9 + - - +
189A ILE* 4.0 7.3 - - - +
190A LEU* 4.3 10.5 - - - +
193A TYR* 4.8 0.2 - - - -
222A THR* 4.0 0.2 - - - -
223A THR* 2.6 50.0 + - - -
240A THR* 1.3 75.7 - - - +
242A HIS* 1.3 62.2 + - - +
243A HIS 4.2 0.2 + - - -
272A SER 3.8 3.4 - - - -
273A TRP* 3.8 17.6 - - - +
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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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186A VAL* 3.9 4.2 - - - +
216A PHE* 3.2 21.3 - + + +
221A TYR 3.7 7.0 - - - +
222A THR* 2.9 39.6 + - + +
240A THR* 2.8 29.1 + - + -
241A SER* 1.3 74.7 + - - +
243A HIS* 1.3 60.5 + - - +
244A LEU* 4.0 12.1 - - + -
271A ASN* 3.3 10.7 - - - +
272A SER* 2.7 50.1 + - - +
602A HFG 2.7 36.0 + - + -
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Residues in contact with HIS 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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179A MET* 3.6 33.2 - - + +
182A ALA* 3.9 20.3 - - + +
183A ALA* 5.0 1.6 - - + -
186A VAL* 4.0 10.5 - - + +
219A GLY* 3.6 2.4 - - - -
220A ASP* 3.2 30.4 + - - +
221A TYR* 3.2 54.2 + + + +
241A SER 4.2 1.0 + - - -
242A HIS* 1.3 73.5 - - - +
244A LEU* 1.3 60.0 + - - +
245A GLY* 3.3 33.8 + - - -
269A TYR* 4.3 7.9 - + - +
270A GLN 3.4 3.8 - - - -
271A ASN* 3.3 18.4 - - - +
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Residues in contact with LEU 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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123A GLU* 5.4 0.9 - - - +
127A TYR* 3.5 25.6 - - + +
216A PHE* 4.1 14.6 - - + -
219A GLY* 4.1 8.3 - - - -
220A ASP* 4.1 6.1 + - - +
242A HIS* 4.0 11.7 - - + -
243A HIS* 1.3 79.1 - - - +
245A GLY* 1.3 66.7 + - - +
247A ASN* 3.0 27.2 + - - +
248A PHE* 3.8 33.7 - - + -
270A GLN* 2.8 29.9 + - + +
271A ASN 3.7 19.1 - - - +
272A SER* 3.9 15.7 - - - +
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Residues in contact with GLY 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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220A ASP* 4.3 7.9 - - - -
243A HIS* 3.3 32.5 + - - -
244A LEU* 1.3 78.0 - - - +
246A GLN* 1.3 60.1 + - - -
249A SER* 4.0 0.7 + - - -
268A ALA 3.4 5.0 - - - +
269A TYR* 3.7 15.5 - - - -
270A GLN* 3.0 26.8 + - - +
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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