Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 5KZX
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 PHE 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PRO* 4.7 5.6 - - + -
160A PHE* 3.3 49.6 - + + -
240A PHE* 3.8 17.5 - + + -
241A PHE* 3.7 2.4 + - - -
242A ALA* 2.7 37.4 + - + +
244A GLN* 1.3 79.7 - - - +
246A LEU* 1.3 62.1 + - - +
247A GLN* 3.7 25.8 - - + -
331A ARG* 3.8 33.9 - - + -
332A SER 3.4 7.2 + - - -
333A THR 4.5 0.6 - - - -
542A PRO* 5.5 0.4 - - + -
543A TYR* 3.6 47.1 - + + -
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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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190A ARG* 4.2 3.8 - - - +
240A PHE 3.4 5.4 - - - +
241A PHE* 4.0 32.5 - - + -
242A ALA 3.3 22.4 - - - +
243A ASP 5.0 0.2 - - - +
245A PHE* 1.3 77.9 - - - +
247A GLN* 1.3 60.2 + - - +
314A ASN* 4.1 4.0 - - - +
330A TRP 3.5 0.7 - - - +
331A ARG* 3.2 5.4 - - - +
332A SER* 2.9 37.2 + - - +
334A GLY 3.2 26.9 - - - +
335A GLY 3.6 8.7 - - - +
336A ILE* 3.5 31.6 - - - +
337A LEU* 4.0 16.6 - - + +
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Residues in contact with GLN 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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90A PHE* 5.8 2.0 - - - +
91A ASP 5.2 2.6 + - - +
94A PRO* 5.1 3.4 - - - +
129A PHE* 4.4 13.7 - - - -
237A ALA* 5.1 2.4 - - - +
238A PRO 3.9 7.5 + - - +
239A LEU* 3.5 10.6 - - - +
240A PHE* 2.9 54.1 + - + +
245A PHE* 3.7 21.6 - - + -
246A LEU* 1.3 74.8 - - - +
248A LEU* 1.3 61.1 + - - +
249A SER* 4.2 18.7 + - - +
329A SER* 4.3 6.3 + - - -
330A TRP 3.1 14.6 - - - +
331A ARG* 2.8 38.9 + - + +
337A LEU* 5.2 0.9 - - - -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 4.1 27.1 - - + -
183A ILE* 4.9 7.0 - - + -
218A PHE* 5.6 2.7 - - + -
220A VAL* 6.4 0.2 - - + -
232A LEU* 6.1 0.2 - - + -
234A THR* 3.8 35.2 - - + +
238A PRO 5.3 1.1 - - - -
239A LEU* 3.9 22.0 - - + +
246A LEU 4.3 0.2 - - - -
247A GLN* 1.3 74.1 - - - +
249A SER* 1.3 61.4 + - - +
329A SER* 3.6 0.4 - - - -
330A TRP* 2.9 50.0 + - + -
337A LEU* 4.1 25.1 - - + +
339A VAL* 4.2 16.8 - - + -
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Residues in contact with SER 249 (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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90A PHE* 4.0 7.7 - - - -
234A THR* 3.0 33.1 + - - +
236A VAL* 4.0 4.5 - - - -
237A ALA* 3.7 31.5 + - - +
238A PRO 5.2 2.9 + - - -
247A GLN* 4.2 8.5 + - - -
248A LEU* 1.3 76.5 - - - +
250A THR* 1.3 63.1 + - - +
328A LEU 3.1 11.7 - - - -
329A SER* 2.7 24.8 + - - -
330A TRP* 5.9 0.7 - - - -
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Residues in contact with THR 250 (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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231A LEU 5.3 0.2 - - - +
232A LEU* 3.4 20.0 - - + -
233A ASN 2.9 31.1 + - - -
234A THR* 4.5 0.9 - - - -
236A VAL* 3.8 6.7 - - - -
249A SER* 1.3 75.8 - - - +
251A SER* 1.3 80.6 + - - +
252A LEU* 4.6 0.7 - - + -
298A TYR* 3.5 24.2 - - - +
327A ALA* 3.2 4.4 - - - +
328A LEU* 2.8 51.2 + - + +
330A TRP* 5.5 3.4 - - + +
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Residues in contact with SER 251 (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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230A VAL* 4.5 10.2 + - - +
231A LEU 3.5 10.8 + - - +
232A LEU 4.6 0.2 - - - -
233A ASN* 3.5 27.9 + - - +
236A VAL* 3.8 16.9 - - - +
250A THR* 1.3 99.3 + - - +
252A LEU* 1.3 63.7 - - - +
326A PRO 3.7 9.4 - - - -
327A ALA* 4.1 3.8 - - - -
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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