Contacts of the strand formed by residues 268 - 276 (chain S) in PDB entry 5K0Y
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 ARG 268 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266S GLU* 3.1 55.5 + - - +
267S PRO* 1.4 87.6 + - - +
269S LEU* 1.3 60.6 + - - +
270S ILE* 5.5 0.4 - - + -
296S ILE* 3.4 20.2 - - - +
297S LEU* 3.5 29.0 + - + +
298S LYS* 2.9 22.9 + - + +
370S VAL* 5.0 7.9 - - + -
371S LEU 3.4 10.8 - - - +
372S GLY* 3.9 4.1 - - - -
373S ALA 3.7 1.8 + - - -
376S ALA* 3.6 18.4 - - - +
377S LEU* 4.0 4.2 - - - +
378S PRO* 3.5 26.8 - - + +
449S GLU* 3.3 37.2 + - + +
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Residues in contact with LEU 269 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268S ARG* 1.3 72.3 - - - +
270S ILE* 1.3 62.1 + - - +
271S VAL* 4.0 13.2 - - + -
292S ALA* 4.9 2.5 - - + -
294S GLY* 3.7 22.9 - - - +
295S SER 3.6 11.7 - - - +
296S ILE* 3.6 26.2 - - + +
301S LEU* 4.5 4.7 - - + -
307S ILE* 3.9 30.4 - - + +
350S ILE* 5.8 0.2 - - + -
352S VAL* 3.8 35.7 - - + -
370S VAL* 4.0 0.5 - - - +
371S LEU* 2.8 48.8 + - + +
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Residues in contact with ILE 270 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163S ALA 5.8 0.2 - - - +
164S VAL* 4.0 22.2 - - + +
268S ARG* 5.3 0.7 - - + -
269S LEU* 1.3 75.5 - - - +
271S VAL* 1.4 66.8 + - - +
272S ILE* 4.0 3.0 + - + +
294S GLY* 3.0 18.7 - - - -
295S SER 2.9 16.9 + - - +
297S LEU* 3.8 39.0 - - + -
368S GLY 5.3 0.2 - - - -
369S GLN 3.6 13.2 - - - +
370S VAL* 4.8 18.8 - - + -
422S GLY* 6.1 1.8 - - - -
423S SER* 3.4 35.7 - - - +
449S GLU* 6.4 2.5 - - + -
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Residues in contact with VAL 271 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269S LEU* 4.0 11.4 - - + -
270S ILE* 1.4 73.8 - - - +
272S ILE* 1.4 64.4 + - - +
273S ARG 3.6 21.1 - - - +
292S ALA* 3.6 30.5 - - + -
293S GLY 3.7 2.2 - - - +
294S GLY* 3.8 4.9 - - - -
366S MET* 3.1 37.0 - - + +
368S GLY* 3.1 13.2 + - - -
369S GLN* 3.0 16.1 + - + +
371S LEU* 3.6 32.1 - - + -
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Residues in contact with ILE 272 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94S LEU* 3.9 19.2 - - + +
146S VAL* 5.0 1.6 - - + -
160S ASN* 4.6 8.7 - - + +
161S GLY* 4.8 6.5 - - - +
164S VAL* 4.1 22.2 - - + -
270S ILE* 4.6 6.3 - - + +
271S VAL* 1.4 75.4 - - - +
273S ARG* 1.4 96.0 + - + +
293S GLY 3.1 13.3 + - - +
294S GLY* 4.6 4.3 - - - -
295S SER 5.3 1.1 - - - +
349S LEU* 4.2 9.0 - - + -
364S ASP* 4.0 1.4 - - - +
366S MET 4.2 0.4 - - - -
367S VAL* 3.5 32.6 - - + +
368S GLY 4.0 7.4 - - - +
423S SER* 3.2 28.3 - - - +
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Residues in contact with ARG 273 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S ARG* 3.7 14.6 - - - +
94S LEU* 3.0 42.0 + - + +
95S GLY 3.1 21.7 + - - -
96S TYR* 3.7 29.6 - - - +
146S VAL* 3.9 12.5 - - - +
271S VAL* 3.6 8.5 - - - +
272S ILE* 1.4 106.1 - - - +
274S SER* 1.4 62.8 + - - +
275S PHE* 3.7 18.5 - - + -
292S ALA* 3.8 0.7 - - - -
293S GLY* 2.9 34.4 + - - +
349S LEU* 3.4 41.6 - - - +
364S ASP* 3.8 4.0 - - - -
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Residues in contact with SER 274 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N C 4.4 3.8 - - - +
74N C 4.1 4.2 - - - +
81S ARG* 3.3 9.2 + - - +
273S ARG* 1.4 70.2 - - - +
275S PHE* 1.4 71.3 + - - +
361S CYS* 4.3 9.5 - - - +
363S ALA 3.4 23.2 - - - -
364S ASP* 3.3 13.3 + - - -
365S ARG 3.2 4.5 + - - -
366S MET* 3.0 50.4 + - - +
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Residues in contact with PHE 275 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N C 3.2 42.4 - - - +
75N A 3.3 36.8 - - - +
81S ARG* 3.7 4.0 - - - -
96S TYR* 3.9 19.1 - + - -
273S ARG* 3.7 34.5 - - + -
274S SER* 1.4 88.3 - - - +
276S ASP* 1.4 60.0 + - - +
277S VAL* 5.2 1.6 - - + -
291S VAL* 2.8 51.1 + - + +
292S ALA 4.6 0.2 - - - -
293S GLY* 3.5 32.5 - - - -
349S LEU* 6.2 0.4 - - + -
351S GLY* 5.5 2.5 - - - -
361S CYS* 3.4 8.2 - - - +
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Residues in contact with ASP 276 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N C 2.9 35.5 + - - +
232P PRO* 3.8 9.9 - - - +
275S PHE* 1.4 73.1 - - - +
277S VAL* 1.3 61.5 + - - +
278S ASN* 3.2 29.5 + - - +
279S LYS* 3.1 24.1 + - - +
289S GLY 4.3 2.6 - - - +
290S GLY* 4.5 1.9 - - - -
291S VAL 4.9 0.7 - - - +
358S PRO* 3.7 30.1 - - - +
361S CYS* 3.6 24.8 + - + +
362S ARG* 4.7 2.7 - - - +
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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