Contacts of the strand formed by residues 357 - 363 (chain A) in PDB entry 3KG2
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 THR 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLN 4.8 0.5 - - - +
247A ILE* 3.3 21.0 - - - +
342A SER 5.2 3.2 + - - +
343A GLY* 5.8 5.9 - - - -
344A ASN 5.7 2.9 - - - +
355A ASN 5.3 0.2 + - - -
356A TYR* 1.3 79.2 + - - +
358A ILE* 1.3 65.0 + - - +
359A ASN* 3.6 20.2 + - - +
373A TYR* 3.6 32.4 - - + -
374A TRP 3.7 3.6 - - - -
375A SER* 5.2 2.3 - - - -
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Residues in contact with ILE 358 (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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115A PRO* 4.6 3.6 - - + -
116A ASP 4.1 9.2 - - - +
117A LEU* 4.2 2.2 - - + -
120A ALA* 4.1 17.7 - - + -
225A LEU* 4.0 22.9 - - + -
245A PHE* 3.7 37.0 - - + -
246A GLN 4.0 8.7 - - - +
247A ILE* 4.0 9.9 - - + -
356A TYR* 3.6 30.7 - - + -
357A THR* 1.3 77.6 - - - +
359A ASN* 1.3 65.6 + - - +
360A ILE* 3.3 5.7 - - - +
374A TRP* 2.8 41.1 + - + +
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Residues in contact with ASN 359 (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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245A PHE* 3.5 3.6 - - - -
246A GLN* 2.9 50.7 + - + +
249A ASP* 3.5 38.3 + - - +
357A THR* 3.6 22.5 - - - +
358A ILE* 1.3 72.7 - - - +
360A ILE* 1.3 61.9 + - - +
361A MET* 3.7 10.2 + - - +
370A LYS* 4.5 13.6 - - + +
372A GLY 3.5 10.8 - - - +
373A TYR* 4.0 4.4 - - - +
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Residues in contact with ILE 360 (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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124A LEU* 3.8 20.4 - - + -
128A TYR* 4.9 1.3 - - - +
244A GLY 3.7 6.7 - - - +
245A PHE* 4.4 16.8 - - + -
358A ILE 3.3 17.0 - - - +
359A ASN* 1.3 70.9 - - - +
361A MET* 1.3 66.9 + - - +
370A LYS* 3.6 3.6 - - - -
371A ILE* 3.0 54.4 + - + -
372A GLY* 2.8 15.6 + - - +
373A TYR* 3.5 21.3 - - - +
374A TRP* 3.6 13.0 - - + -
380A MET* 3.6 26.9 - - + -
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Residues in contact with MET 361 (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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227A PHE* 3.3 25.6 - - + -
228A THR* 4.2 11.9 - - + -
243A SER* 3.2 8.0 - - - -
244A GLY 3.0 31.0 + - - +
246A GLN* 3.6 33.4 - - + +
359A ASN* 3.8 8.7 - - - +
360A ILE* 1.3 77.1 - - - +
362A GLU* 1.3 63.6 + - - +
368A PRO* 3.9 14.8 - - + -
369A ARG* 3.7 25.4 - - - +
370A LYS* 3.7 27.8 - - + +
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Residues in contact with GLU 362 (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* 4.7 2.1 + - - -
128A TYR* 2.7 38.9 + - - +
219A HIS* 5.4 0.4 + - - -
227A PHE* 4.4 4.3 - - - -
241A GLU* 5.5 5.3 - - - +
242A VAL 3.5 4.0 - - - +
243A SER* 3.7 6.5 - - - +
361A MET* 1.3 76.1 - - - +
363A LEU* 1.3 62.9 + - - +
364A LYS* 3.6 2.3 + - + +
368A PRO* 3.5 1.0 - - - +
369A ARG* 2.9 34.8 + - + +
371A ILE* 3.3 36.2 - - + +
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Residues in contact with LEU 363 (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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227A PHE* 4.1 6.9 - - + -
232A LEU* 3.6 23.6 - - + -
235A ILE* 3.4 35.4 - - + +
236A GLN* 3.6 41.2 - - + +
240A ALA 5.4 1.6 - - - +
241A GLU* 5.3 3.3 - - - +
242A VAL* 2.9 32.5 + - + +
362A GLU* 1.3 71.3 - - - +
364A LYS* 1.3 58.9 + - - +
367A GLY 3.7 3.8 - - - -
368A PRO* 3.6 32.3 - - + -
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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