Contacts of the strand formed by residues 337 - 342 (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 LEU 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PHE* 5.5 0.6 - - + -
182A THR* 3.2 5.5 - - - -
183A ILE* 2.8 57.0 + - + +
239A LEU* 3.7 30.1 - - + -
241A PHE* 4.2 13.2 - - + -
246A LEU* 4.0 29.6 - - + +
247A GLN 5.0 0.7 - - - +
248A LEU* 4.1 27.6 - - + +
312A LEU* 4.1 24.7 - - + -
314A ASN* 5.7 0.2 - - - +
330A TRP* 5.5 2.5 - - + -
332A SER* 5.9 0.7 - - - -
336A ILE* 1.3 74.3 - - - +
338A ASP* 1.3 59.3 + - - +
339A VAL* 4.1 8.7 - - + -
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Residues in contact with ASP 338 (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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180A HIS* 2.6 32.1 + - - -
181A PHE 3.7 2.7 - - - -
182A THR* 3.6 8.4 - - - +
192A GLU* 4.7 1.6 - - - +
311A PHE 3.6 0.9 - - - +
312A LEU* 3.4 6.5 - - - +
313A LEU* 2.7 70.2 + - - +
336A ILE* 3.6 16.7 + - + +
337A LEU* 1.3 72.5 - - - +
339A VAL* 1.3 58.9 + - - +
340A TYR* 3.7 3.5 + - - -
1020A PGE 3.5 21.7 - - - -
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Residues in contact with VAL 339 (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 LEU 4.0 0.3 - - - +
180A HIS* 3.2 4.9 - - - -
181A PHE* 2.8 79.4 + - + +
232A LEU* 5.2 2.9 - - + -
248A LEU* 4.2 13.9 - - + -
310A VAL* 3.9 25.4 - - + -
311A PHE 3.5 3.4 - - - +
312A LEU* 3.8 19.3 - - + -
330A TRP* 5.8 2.5 - - - +
337A LEU* 4.4 3.6 - - + -
338A ASP* 1.3 81.6 + - - +
340A TYR* 1.3 64.7 + - - +
341A ILE* 3.9 10.0 - - + +
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Residues in contact with TYR 340 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU* 3.9 10.3 - - - -
178A ARG* 3.8 19.7 - - + -
179A LEU 3.4 3.1 - - - -
180A HIS* 3.2 47.6 - + + -
195A LEU* 4.2 15.9 - - - +
197A THR* 5.1 6.8 - - - +
198A PRO* 5.6 4.7 - - + +
310A VAL* 3.2 7.8 - - - +
311A PHE* 2.9 50.6 + + + +
313A LEU* 4.3 16.2 - - + +
338A ASP* 3.7 9.7 + - - -
339A VAL* 1.3 76.4 - - - +
341A ILE* 1.3 63.3 + - - +
342A PHE* 3.5 24.1 - + + -
357A VAL* 4.0 25.7 - - + +
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Residues in contact with ILE 341 (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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177A ASN 3.5 1.4 - - - +
178A ARG* 3.4 5.5 - - - -
179A LEU* 2.7 60.1 + - + +
181A PHE* 3.8 35.2 - - + -
222A VAL* 4.6 13.0 - - + -
231A LEU* 5.5 2.2 - - + -
232A LEU* 4.2 18.2 - - + -
308A HIS* 4.3 17.3 - - + -
309A GLY 3.3 8.3 - - - +
310A VAL* 4.5 8.1 - - + -
339A VAL* 3.9 7.9 - - + +
340A TYR* 1.3 80.3 - - - +
342A PHE* 1.3 64.7 + - - +
343A LEU* 3.8 19.6 - - + +
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Residues in contact with PHE 342 (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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177A ASN 3.4 2.9 - - - -
178A ARG* 3.8 17.7 - - + -
297A PHE* 4.1 9.2 - + - -
308A HIS* 3.1 9.7 - - - +
309A GLY 2.8 49.3 + - - +
311A PHE* 3.8 24.5 - - + -
340A TYR* 3.5 24.7 - + + -
341A ILE* 1.3 74.3 - - - +
343A LEU* 1.3 60.7 + - - +
344A GLY 3.5 1.7 + - - -
350A VAL* 4.2 7.9 - - + +
353A GLN* 3.4 44.0 - - + +
354A TYR* 3.7 27.8 - + + -
357A VAL* 3.6 20.9 - - + -
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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