Contacts of the strand formed by residues 269 - 276 (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 TYR 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ALA* 3.3 1.6 - - - -
176A PHE* 2.6 44.2 + - - -
177A ALA 3.2 26.5 - - - -
178A THR* 3.3 24.9 - - - +
179A MET* 3.5 29.7 - - + -
182A ALA* 4.1 12.1 - - + -
243A HIS* 4.3 4.5 - + - +
245A GLY* 3.4 20.4 - - - -
246A GLN* 3.3 41.0 + - + -
266A GLN* 5.3 3.4 + - + -
267A PHE 4.5 0.7 - - - -
268A ALA* 1.3 74.5 - - - +
270A GLN* 1.3 59.5 + - - +
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Residues in contact with GLN 270 (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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127A TYR* 3.8 27.2 - - - +
130A TYR* 4.8 4.2 - - - -
174A SER 3.3 11.4 - - - +
175A ALA* 3.9 10.5 - - + -
182A ALA* 4.8 0.4 - - - -
243A HIS* 3.4 3.7 - - - -
244A LEU* 2.8 44.6 + - + -
245A GLY 3.0 10.8 + - - +
248A PHE* 3.1 16.2 + - - +
249A SER* 3.0 30.5 + - - -
254A ILE* 3.2 30.4 - - + +
268A ALA* 4.4 4.3 - - + +
269A TYR* 1.3 79.4 - - - +
271A ASN* 1.3 65.7 + - - +
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Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.9 2.8 + - - -
173A HIS* 3.7 3.1 - - - -
174A SER* 2.9 37.6 + - - +
176A PHE* 3.5 5.2 - - - -
182A ALA* 2.6 35.1 + - - +
185A GLU* 3.1 22.2 + - - +
186A VAL* 3.1 22.8 - - - +
242A HIS 3.3 6.1 - - - +
243A HIS* 3.3 14.7 - - - -
244A LEU* 3.7 10.1 - - - +
270A GLN* 1.3 83.5 - - - +
272A SER* 1.3 66.1 + - - +
273A TRP* 4.0 3.8 - - + +
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Residues in contact with SER 272 (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* 4.1 4.7 + - - -
127A TYR* 4.2 5.6 - - - -
172A GLY 3.1 14.4 - - - -
173A HIS* 3.9 17.0 - - - -
242A HIS* 2.7 40.0 + - - +
244A LEU* 3.9 16.6 - - - +
271A ASN* 1.3 80.9 - - - +
273A TRP* 1.3 60.8 + - - +
602A HFG 3.5 24.1 + - - +
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Residues in contact with TRP 273 (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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64A PHE* 4.2 7.2 - + - -
68A ILE* 4.3 3.4 - - + -
73A VAL* 4.3 28.3 - - + -
144A LEU 5.1 0.2 - - - -
145A ASN* 3.9 6.1 - - - -
170A GLN* 3.2 32.3 + - - -
171A GLU* 3.5 2.3 - - - -
172A GLY* 2.9 55.1 + - - -
173A HIS 4.6 1.1 - - - -
174A SER* 3.7 9.7 + - - -
185A GLU* 2.8 36.9 + - - -
186A VAL* 5.4 0.7 - - - -
189A ILE* 3.7 41.7 - - + -
193A TYR* 3.3 11.4 + - - +
240A THR 3.3 14.4 - - - +
241A SER* 3.8 13.7 - - - -
271A ASN* 4.0 4.2 - - + +
272A SER* 1.3 87.3 - - - +
274A GLY* 1.3 58.6 + - - +
602A HFG 3.8 8.9 - - - +
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Residues in contact with GLY 274 (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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169A TRP* 4.9 5.4 - - - -
170A GLN 3.3 12.1 - - - -
193A TYR* 3.1 14.6 + - - -
239A GLY* 3.6 1.9 - - - -
240A THR* 3.1 31.8 + - - -
273A TRP* 1.3 74.6 - - - +
275A LEU* 1.3 57.8 + - - +
276A THR* 5.3 2.2 - - - -
602A HFG 3.8 14.1 - - - +
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Residues in contact with LEU 275 (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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57A TRP* 3.9 8.1 - - + -
60A ILE* 4.2 16.2 - - + -
64A PHE* 5.2 3.8 - - + -
147A TRP* 6.3 2.2 - - + -
169A TRP* 3.3 2.6 - - - +
170A GLN* 2.9 39.8 + - + +
193A TYR* 3.4 27.1 - - + -
196A VAL* 4.2 26.5 - - + -
197A TYR* 3.8 9.0 - - + -
238A GLY 3.3 25.4 - - - +
239A GLY* 4.2 4.3 - - - -
274A GLY* 1.3 73.4 - - - -
276A THR* 1.3 72.7 + - - +
279A THR* 3.8 19.3 - - + -
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Residues in contact with THR 276 (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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57A TRP* 3.7 8.2 - - - -
167A PHE* 3.5 31.0 - - + -
168A LEU 3.8 9.2 - - - -
169A TRP* 3.6 18.4 - - + +
238A GLY 4.8 1.8 + - - -
274A GLY 5.3 0.9 - - - -
275A LEU* 1.3 84.4 - - - +
277A THR* 1.3 54.2 + - - +
278A ARG* 3.0 36.8 + - - +
279A THR* 2.6 31.2 + - - +
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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